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ORCIDJournal of Chemical Information and Modeling, Volume 64
Volume 64, Number 1, January 2024
- Issue Publication Information.
- Issue Editorial Masthead.
- Kenneth M. Merz Jr.
:
In Memoriam: Dr. George W. A. Milne. 1-2 - Andrew Rusinko III, Mohammad A. Rezaei, Lukas Friedrich, Hans-Peter Buchstaller, Daniel Kuhn, Ashwini Ghogare:
AIDDISON: Empowering Drug Discovery with AI/ML and CADD Tools in a Secure, Web-Based SaaS Platform. 3-8 - Esther Heid, Kevin P. Greenman, Yunsie Chung, Shih-Cheng Li, David E. Graff, Florence H. Vermeire, Haoyang Wu, William H. Green Jr., Charles McGill:
Chemprop: A Machine Learning Package for Chemical Property Prediction. 9-17 - Oleg Mikhailovskii, Sergei A. Izmailov, Yi Xue, David A. Case, Nikolai R. Skrynnikov:
X-ray Crystallography Module in MD Simulation Program Amber 2023. Refining the Models of Protein Crystals. 18-25 - Raphaelle Versini, Sujith Sritharan, Burcu Aykaç Fas, Thibault Tubiana, Sana Zineb Aimeur, Julien Henri, Marie Erard, Oliver Nüsse, Jessica Andreani, Marc Baaden, Patrick Fuchs, Tatiana Galochkina, Alexios Chatzigoulas, Zoe Cournia, Hubert Santuz, Sophie Sacquin-Mora, Antoine Taly:
A Perspective on the Prospective Use of AI in Protein Structure Prediction. 26-41 - Varvara Voinarovska, Mikhail Kabeshov, Dmytro Dudenko, Samuel Genheden, Igor V. Tetko:
When Yield Prediction Does Not Yield Prediction: An Overview of the Current Challenges. 42-56 - Zhuohang Yu, Zengrui Wu, Ze Wang, Yimeng Wang, Moran Zhou, Weihua Li, Guixia Liu, Yun Tang:
Network-Based Methods and Their Applications in Drug Discovery. 57-75 - Chunxiang Peng, Fang Liang, Yuhao Xia, Kai-Long Zhao, Minghua Hou, Gui-Jun Zhang:
Recent Advances and Challenges in Protein Structure Prediction. 76-95 - Ning-Ning Wang, Bei Zhu, Xin-Liang Li, Shao Liu, Jian-Yu Shi, Dong-Sheng Cao:
Comprehensive Review of Drug-Drug Interaction Prediction Based on Machine Learning: Current Status, Challenges, and Opportunities. 96-109 - Ruihan Zhang, Xingran Xie, Dongxuan Ni, Hairong Wang, Jin Li, Weilie Xiao:
MT-EpiPred: Multitask Learning for Prediction of Small-Molecule Epigenetic Modulators. 110-118 - Yuto Matsumoto, Hiroaki Gotoh:
Compound Classification and Consideration of Correlation with Chemical Descriptors from Articles on Antioxidant Capacity Using Natural Language Processing. 119-127 - Arnab Bose, Gabriel A. Valdivia-Berroeta, Nina C. Gonnella:
Predicting Autoxidation of Sulfides in Drug-like Molecules Using Quantum Mechanical/Density Functional Theory Methods. 128-137 - Jiwon Seo, Ravi Singh, Jonghyuk Ryu, Jun-Ho Choi:
Molecular Aggregation Behavior and Microscopic Heterogeneity in Binary Osmolyte-Water Solutions. 138-149 - Kwangho Nam, Abdul Raafik Arattu Thodika, Christin Grundström, Uwe H. Sauer, Magnus Wolf-Watz:
Elucidating Dynamics of Adenylate Kinase from Enzyme Opening to Ligand Release. 150-163 - Alejandro Rivera-Pousa, Raúl Lois-Cuns, Martín Otero-Lema, Hadrián Montes-Campos, Trinidad Méndez-Morales, Luis M. Varela:
Size Matters: A Computational Study of Hydrogen Absorption in Ionic Liquids. 164-177 - Gaurav Jhaa, Pattath D. Pancharatna, Musiri M. Balakrishnarajan:
Alternatives for Epoxides in Graphene Oxide. 178-188 - Aitor Valdivia, F. Javier Luque, Salomé Llabrés:
Binding of Cholesterol to the N-Terminal Domain of the NPC1L1 Transporter: Analysis of the Epimerization-Related Binding Selectivity and Loop Mutations. 189-204 - Jacqueline C. Calderón, Eva Plut, Max Keller, Chiara Cabrele, Oliver Reiser, Francesco L. Gervasio, Timothy Clark:
Extended Metadynamics Protocol for Binding/Unbinding Free Energies of Peptide Ligands to Class A G-Protein-Coupled Receptors. 205-218 - Florian Flachsenberg, Christiane Ehrt, Torben Gutermuth, Matthias Rarey:
Redocking the PDB. 219-237 - Zhong-Hao Ren, Chang-Qing Yu, Li-Ping Li, Zhu-Hong You, Zheng-Wei Li, Shanwen Zhang, Xiangxiang Zeng, Yi-Fan Shang:
SiSGC: A Drug Repositioning Prediction Model Based on Heterogeneous Simplifying Graph Convolution. 238-249 - Lieyang Chen, Yujie Wu, Chuanjie Wu, Ana Silveira, Woody Sherman, Huafeng Xu, Emilio Gallicchio:
Performance and Analysis of the Alchemical Transfer Method for Binding-Free-Energy Predictions of Diverse Ligands. 250-264 - Toby E. King, James R. Humphrey, Charles A. Laughton, Neil R. Thomas, Jonathan D. Hirst:
Optimizing Excipient Properties to Prevent Aggregation in Biopharmaceutical Formulations. 265-275 - Afshin Zamani Zakaria, Alpeshkumar K. Malde, Tim Gould:
Permeability of Dermatological Solutes through the Short Periodicity Phase of Human Stratum Corneum Lipid Bilayers. 276-288 - Bing Rao, Xuan Yu, Jie Bai, Jun Hu:
E2EATP: Fast and High-Accuracy Protein-ATP Binding Residue Prediction via Protein Language Model Embedding. 289-300 - Jiaxuan Li, Lei Wang, Zefeng Zhu, Chen Song:
Exploring the Alternative Conformation of a Known Protein Structure Based on Contact Map Prediction. 301-315 - Haoqing Yu, Ruheng Wang, Jianbo Qiao, Leyi Wei:
Multi-CGAN: Deep Generative Model-Based Multiproperty Antimicrobial Peptide Design. 316-326
Volume 64, Number 2, January 2024
- Issue Publication Information.
- Issue Editorial Masthead.
- Jawad Chowdhury, Charles Fricke, Olajide Bamidele, Mubarak Bello, Wenqiang Yang, Andreas Heyden, Gabriel Terejanu:
Invariant Molecular Representations for Heterogeneous Catalysis. 327-339 - Gen Li, Sijie Yao, Long Fan:
ProSTAGE: Predicting Effects of Mutations on Protein Stability by Using Protein Embeddings and Graph Convolutional Networks. 340-347 - Ya Chen, Thomas Seidel, Roxane Axel Jacob, Steffen Hirte, Angelica Mazzolari, Alessandro Pedretti, Giulio Vistoli, Thierry Langer, Filip Miljkovic, Johannes Kirchmair:
Active Learning Approach for Guiding Site-of-Metabolism Measurement and Annotation. 348-358 - Yu Yin, Zhen Yang, Na Li, Xuan Yu, Mei-ling Chen, Meng Wang, Xiao-liang Ren:
Least Absolute Shrinkage and Selection Operator-Based Prediction of the Binding Constant of p-Sulfonatocalix[6]/[8]arenes with Alkaloids. 359-377 - Julian M. Delgado, Péter R. Nagy, Sameer Varma:
Polarizable AMOEBA Model for Simulating Mg2+·Protein·Nucleotide Complexes. 378-392 - Mateus Sá Magalhães Serafim, Thales Kronenberger, Rafael Eduardo Oliveira Rocha, Amanda Del Rio Abreu Rosa, Thaysa Lara Gonçalves Mello, Antti Poso, Rafaela Salgado Ferreira, Jonatas Santos Abrahão, Erna Geessien Kroon, Bruno Eduardo Fernandes Mota, Vinicius Gonçalves Maltarollo:
Aminopyrimidine Derivatives as Multiflavivirus Antiviral Compounds Identified from a Consensus Virtual Screening Approach. 393-411 - Marco Foscato, Giovanni Occhipinti, Sondre H. Eliasson, Vidar R. Jensen:
Automated de Novo Design of Olefin Metathesis Catalysts: Computational and Experimental Analysis of a Simple Thermodynamic Design Criterion. 412-424 - Matthew S. Smith, Ian S. Knight, Rian C. Kormos, Joseph G. Pepe, Peter Kunach, Marc I. Diamond, Sarah H. Shahmoradian, John J. Irwin, William F. Degrado, Brian K. Shoichet:
Docking for Molecules That Bind in a Symmetric Stack with SymDOCK. 425-434 - William T. Higgins, Sandip Vibhute, Chad Bennett, Steffen Lindert:
Discovery of Nanomolar Inhibitors for Human Dihydroorotate Dehydrogenase Using Structure-Based Drug Discovery Methods. 435-448 - Midhun K. Madhu, Kunal Shewani, Rajesh K. Murarka:
Biased Signaling in Mutated Variants of β2-Adrenergic Receptor: Insights from Molecular Dynamics Simulations. 449-469 - Amanda C. Macke, Jacob E. Stump, Maria S. Kelly, Jamie Rowley, Vageesha Herath, Sarah Mullen, Ruxandra I. Dima:
Searching for Structure: Characterizing the Protein Conformational Landscape with Clustering-Based Algorithms. 470-482 - Deepak Ahire, Charles Mariasoosai, Siavosh Naji-Talakar, Senthil Natesan, Bhagwat Prasad:
Promiscuity and Quantitative Contribution of UGT2B17 in Drug and Steroid Metabolism Determined by Experimental and Computational Approaches. 483-498 - Maya Petgrave, Shubham Devesh Ramgoolam, Aravindhan Ganesan:
Deciphering the Molecular Association of Human CRIP1a with an Agonist-Bound Cannabinoid Receptor 1. 499-517 - Charlotte Bouquiaux, Benoît Champagne, Pierre Beaujean:
Multimillion Atom Simulations of Di-8-ANEPPS Chromophores Embedded in a Model Plasma Membrane: Toward the Investigation of Realistic Dyed Cell Membranes. 518-531 - Yusuke Miyazaki, Wataru Shinoda:
pSPICA Force Field Extended for Proteins and Peptides. 532-542 - Santiago Antolínez, Peter Eugene Jones, James C. Phillips, Jodi A. Hadden-Perilla:
AMBERff at Scale: Multimillion-Atom Simulations with AMBER Force Fields in NAMD. 543-554 - Juan I. Felice, Verónica Milesi, Gabriel Fabricius:
Exploration of the Parameter Space of an Ion Channel Kinetic Model by a Markov-Chain-Based Methodology. 555-562
Volume 64, Number 3, February 2024
- Issue Editorial Masthead.
- Issue Publication Information.
- Jinlu Zhang, Yin Fang, Xin Shao, Huajun Chen, Ningyu Zhang, Xiaohui Fan:
The Future of Molecular Studies through the Lens of Large Language Models. 563-566 - Anton Jansen, Noora Aho, Gerrit Groenhof, Pavel Buslaev, Berk Hess:
phbuilder: A Tool for Efficiently Setting up Constant pH Molecular Dynamics Simulations in GROMACS. 567-574 - Tao Shen, Jiale Guo, Zunsheng Han, Gao Zhang, Qingxin Liu, Xinxin Si, Dongmei Wang, Song Wu, Jie Xia:
AutoMolDesigner for Antibiotic Discovery: An AI-Based Open-Source Software for Automated Design of Small-Molecule Antibiotics. 575-583 - Mariona Torrens-Fontanals, Panagiotis Tourlas, Stefan Doerr, Gianni De Fabritiis:
PlayMolecule Viewer: A Toolkit for the Visualization of Molecules and Other Data. 584-589 - Robert I. Horne, Jared Wilson-Godber, Alicia González Díaz, Z. Faidon Brotzakis, Srijit Seal, Rebecca C. Gregory, Andrea Possenti, Sean Chia, Michele Vendruscolo:
Using Generative Modeling to Endow with Potency Initially Inert Compounds with Good Bioavailability and Low Toxicity. 590-596 - Andre Nicolle, Sili Deng, Matthias Ihme, Nursulu Kuzhagaliyeva, Emad Al Ibrahim, Aamir Farooq:
Mixtures Recomposition by Neural Nets: A Multidisciplinary Overview. 597-620 - Parveen Gartan, Fahimeh Khorsand, Pushpak Mizar, Juha Ilmari Vahokovski, Luis F. Cervantes, Bengt Erik Haug, Ruth Brenk, Charles L. Brooks III, Nathalie Reuter:
Investigating Polypharmacology through Targeting Known Human Neutrophil Elastase Inhibitors to Proteinase 3. 621-626 - Hongshuo Huang, Rishikesh Magar, Amir Barati Farimani:
Pretraining Strategies for Structure Agnostic Material Property Prediction. 627-637 - Surya Prakash Tiwari, Wei Shi, Samir Budhathoki, James Baker, Ali K. Sekizkardes, Lingxiang Zhu, Victor A. Kusuma, David P. Hopkinson, Janice A. Steckel:
Creation of Polymer Datasets with Targeted Backbones for Screening of High-Performance Membranes for Gas Separation. 638-652 - Gregory W. Kyro, Anton Morgunov, Rafael I. Brent, Victor S. Batista:
ChemSpaceAL: An Efficient Active Learning Methodology Applied to Protein-Specific Molecular Generation. 653-665 - Hao Zhang, Jinchao Huang, Junjie Xie, Weifeng Huang, Yuedong Yang, Mingyuan Xu, Jinping Lei, Hongming Chen:
GRELinker: A Graph-Based Generative Model for Molecular Linker Design with Reinforcement and Curriculum Learning. 666-676 - Hyeonsu Kim, Kyunghoon Lee, Jun Hyeong Kim, Woo Youn Kim:
Deep Learning-Based Chemical Similarity for Accelerated Organic Light-Emitting Diode Materials Discovery. 677-689 - Lewis Y. Geer, Stephen E. Stein, William Gary Mallard, Douglas J. Slotta:
AIRI: Predicting Retention Indices and Their Uncertainties Using Artificial Intelligence. 690-696 - Prudencio Tossou, Cas Wognum, Michael Craig, Hadrien Mary, Emmanuel Noutahi:
Real-World Molecular Out-Of-Distribution: Specification and Investigation. 697-711 - Alec J. Sanchez, Sarah Maier, Krishnan Raghavachari:
Leveraging DFT and Molecular Fragmentation for Chemically Accurate pKa Prediction Using Machine Learning. 712-723 - Minfei Ma, Xinben Zhang, Liping Zhou, Zijian Han, Yulong Shi, Jintian Li, Leyun Wu, Zhijian Xu, Weiliang Zhu:
D3Rings: A Fast and Accurate Method for Ring System Identification and Deep Generation of Drug-Like Cyclic Compounds. 724-736 - Weichen Bo, Yangqin Duan, Yurong Zou, Ziyan Ma, Tao Yang, Peng Wang, Tao Guo, Zhiyuan Fu, Jianmin Wang, Linchuan Fan, Jie liu, Taijin Wang, Lijuan Chen:
Local Scaffold Diversity-Contributed Generator for Discovering Potential NLRP3 Inhibitors. 737-748 - Susanta Das, Kenneth M. Merz Jr.:
Molecular Gas-Phase Conformational Ensembles. 749-760 - Qing Wang, Xuegang Fu, Yuting Yan, Tao Liu, Yuting Xie, Xiaoqing Song, Yu Zhou, Min Xu, Ping Wang, Peng Fu, Jianhui Huang, Niu Huang:
Structure-Based Identification of Organoruthenium Compounds as Nanomolar Antagonists of Cannabinoid Receptors. 761-774 - Justin K. Kirkland, Jugal Kumawat, Maliheh Shaban Tameh, Tyson Tolman, Allison C. Lambert, Graham R. Lief, Qing Yang, Daniel H. Ess:
Machine Learning Models for Predicting Zirconocene Properties and Barriers. 775-784 - Mingqiong Tong, Peng Liu, Chaoqun Li, Zhongyu Zhang, Wan Sun, Pingxuan Dong, Na Fan, Xiaoyue Wang, Jing Liu, Chao Lv, Zanxia Cao, Yan Wang:
Interaction of Asn297-Linked Glycan Ligands with the Fc Fragment of the Immunoglobulin Class G1: A Molecular Dynamics Simulation Study. 785-798 - Jyotirmoy Deb, Lakshi Saikia, Kripa Dristi Dihingia, G. Narahari Sastry:
ChatGPT in the Material Design: Selected Case Studies to Assess the Potential of ChatGPT. 799-811 - Luke Landry, Pengfei Li:
Development of a Fluctuating Charge Model for Zinc-Containing Metalloproteins. 812-824 - Christian Hölzer, Igor Gordiy, Stefan Grimme, Markus Bursch:
Hybrid DFT Geometries and Properties for 17k Lanthanoid Complexes─The LnQM Data Set. 825-836 - Shalmali Kharche, Manjul Yadav, Vrushali Hande, Shikha Prakash, Durba Sengupta:
Improved Protein Dynamics and Hydration in the Martini3 Coarse-Grain Model. 837-850 - Xu Zhou, Zhiqiang Wei, Hao Lu, Jiaqi He, Yuan Gao, Xiaotong Hu, Cunji Wang, Yujie Dong, Hao Liu:
Large-Scale Molecular Dynamics Simulation Based on Heterogeneous Many-Core Architecture. 851-861 - Nurit Haspel, Hyunbum Jang, Ruth Nussinov:
Allosteric Activation of RhoA Complexed with p115-RhoGEF Deciphered by Conformational Dynamics. 862-873 - Nopawit Khamto, Kraikrit Utama, Panida Boontawee, Atchara Janthong, Suriya Tatieng, Supakorn Arthan, Vachira Choommongkol, Padchanee Sangthong, Chavi Yenjai, Nuttee Suree, Puttinan Meepowpan:
Inhibitory Activity of Flavonoid Scaffolds on SARS-CoV-2 3CLpro: Insights from the Computational and Experimental Investigations. 874-891 - Simone Albani, Elisa Costanzi, Gia Linh Hoang, Maria Kuzikov, Marcus Frings, Narjes Ansari, Nicola Demitri, Toan T. Nguyen, Valerio Rizzi, Jörg B. Schulz, Carsten Bolm, Andrea Zaliani, Paolo Carloni, Paola Storici, Giulia Rossetti:
Unexpected Single-Ligand Occupancy and Negative Cooperativity in the SARS-CoV-2 Main Protease. 892-904 - Sayyed Jalil Mahdizadeh, Michael Stier, Antonio Carlesso, Aurore Lamy, Melissa Thomas, Leif A. Eriksson:
Multiscale In Silico Study of the Mechanism of Activation of the RtcB Ligase by the PTP1B Phosphatase. 905-917 - Anna P. Tolstova, Alexander A. Makarov, Alexei A. Adzhubei:
Structure Comparison of Beta Amyloid Peptide Aβ 1-42 Isoforms. Molecular Dynamics Modeling. 918-932 - Christopher Kang, Alyson Shoji, Christophe Chipot, Rui Sun:
Impact of the Unstirred Water Layer on the Permeation of Small-Molecule Drugs. 933-943 - Rajwinder Kaur, Stacey D. Wetmore:
Is Metal Stabilization of the Leaving Group Required or Can Lysine Facilitate Phosphodiester Bond Cleavage in Nucleic Acids? A Computational Study of EndoV. 944-959 - Ayse A. Bekar-Cesaretli, Omeir Khan, Thu Nguyen, Dima Kozakov, Diane Joseph-McCarthy, Sandor Vajda:
Conservation of Hot Spots and Ligand Binding Sites in Protein Models by AlphaFold2. 960-973 - Yunhao Mei, Yong Shen:
Cation-π Interactions Greatly Influence Ion Transportability of the Light-Driven Sodium Pump KR2: A Molecular Dynamics Study. 974-982 - Anupom Roy, Mikko Karttunen:
A Molecular Dynamics Simulation Study of the Effects of βGln114 Mutation on the Dynamic Behavior of the Catalytic Site of the Tryptophan Synthase. 983-1003 - Ian S. Knight, Olivier Mailhot, Khanh G. Tang, John J. Irwin:
DockOpt: A Tool for Automatic Optimization of Docking Models. 1004-1016 - Sana Akhter, Zhichao Tang, Jinan Wang, Mercy Haboro, Erik D. Holmstrom, Jingxin Wang, Yinglong Miao:
Mechanism of Ligand Binding to Theophylline RNA Aptamer. 1017-1029 - Zora Novakova, Zahra Aliakbar Tehrani, Radek Jurok, Lucia Motlova, Zsófia Kutil, Jiri Pavlicek, Shivam Shukla, Cindy J. Choy, Barbora Havlinova, Petra Baranova, Clifford E. Berkman, Martin Kuchar, Jirí Cerný, Cyril Barinka:
Structural, Biochemical, and Computational Characterization of Sulfamides as Bimetallic Peptidase Inhibitors. 1030-1042 - Zi Liu, Chengxin Zhang, Qidi Zhang, Yang Zhang, Dong-Jun Yu:
TM-search: An Efficient and Effective Tool for Protein Structure Database Search. 1043-1049 - Jiashuo Zhang, Ruheng Wang, Leyi Wei:
MucLiPred: Multi-Level Contrastive Learning for Predicting Nucleic Acid Binding Residues of Proteins. 1050-1065 - Shuang Guo, Yuwei Liu, Yue Sun, Hanxiao Zhou, Yue Gao, Peng Wang, Hui Zhi, Yakun Zhang, Jing Gan, Shangwei Ning:
Metabolic-Related Gene Prognostic Index for Predicting Prognosis, Immunotherapy Response, and Candidate Drugs in Ovarian Cancer. 1066-1080 - Emma Goulard Coderc de Lacam, Benoît Roux, Christophe Chipot:
Classifying Protein-Protein Binding Affinity with Free-Energy Calculations and Machine Learning Approaches. 1081-1091 - Guolun Zhong, Lei Deng:
ACPScanner: Prediction of Anticancer Peptides by Integrated Machine Learning Methodologies. 1092-1104 - Farzad Molani, Simon Webb, Art E. Cho:
Correction to "Combining QM/MM Calculations with Classical Mining Minima to Predict Protein-Ligand Binding Free Energy". 1105 - Shan Sun, Makoto Fushimi, Thomas Rossetti, Navpreet Kaur, Jacob Ferreira, Michael Miller, Jonathan Quast, Joop van den Heuvel, Clemens Steegborn, Lonny R. Levin, Jochen Buck, Robert W. Myers, Stacia Kargman, Nigel Liverton, Peter T. Meinke, David J. Huggins:
Addition to "Scaffold Hopping and Optimization of Small Molecule Soluble Adenyl Cyclase Inhibitors Led by Free Energy Perturbation". 1106
Volume 64, Number 4, February 2024
- Issue Publication Information.
- Issue Editorial Masthead.
- Ronaldo C. Prati, Bruno S. M. Rodrigues, Iberis Aragão, Thereza A. Soares, Marcos G. Quiles, Juarez L. F. Da Silva:
The Impact of Interdisciplinary, Gender and Geographic Distributions on the Citation Patterns of the Journal of Chemical Information and Modeling. 1107-1111 - Yanqiao Zhu, Dingshuo Chen, Yuanqi Du, Yingze Wang, Qiang Liu, Shu Wu:
Molecular Contrastive Pretraining with Collaborative Featurizations. 1112-1122 - Benson Chen, Mohammad M. Sultan, Theofanis Karaletsos:
Compositional Deep Probabilistic Models of DNA-Encoded Libraries. 1123-1133 - Seongwon Kim, Parisa Mollaei, Akshay Antony, Rishikesh Magar, Amir Barati Farimani:
GPCR-BERT: Interpreting Sequential Design of G Protein-Coupled Receptors Using Protein Language Models. 1134-1144 - Benjamin Kaufman, Edward C. Williams, Carl Underkoffler, Ryan Pederson, Narbe Mardirossian, Ian Watson, John Parkhill:
COATI: Multimodal Contrastive Pretraining for Representing and Traversing Chemical Space. 1145-1157 - Kathryn Klarich, Brian Goldman, Trevor Kramer, Patrick Riley, W. Patrick Walters:
Thompson Sampling─An Efficient Method for Searching Ultralarge Synthesis on Demand Databases. 1158-1171 - Srijit Seal, Ola Spjuth, Layla Hosseini-Gerami, Miguel García-Ortegón, Shantanu Singh, Andreas Bender, Anne E. Carpenter:
Insights into Drug Cardiotoxicity from Biological and Chemical Data: The First Public Classifiers for FDA Drug-Induced Cardiotoxicity Rank. 1172-1186 - Son Gyo Jung, Guwon Jung, Jacqueline M. Cole:
Automatic Prediction of Band Gaps of Inorganic Materials Using a Gradient Boosted and Statistical Feature Selection Workflow. 1187-1200 - Frédéric Célerse, Matthew D. Wodrich, Sergi Vela, Simone Gallarati, Raimon Fabregat, Veronika Jurásková, Clémence Corminboeuf:
From Organic Fragments to Photoswitchable Catalysts: The OFF-ON Structural Repository for Transferable Kernel-Based Potentials. 1201-1212 - Mingyang Wang, Zhengjian Wu, Jike Wang, Gaoqi Weng, Yu Kang, Peichen Pan, Dan Li, Yafeng Deng, Xiaojun Yao, Zhitong Bing, Chang-Yu Hsieh, Tingjun Hou:
Genetic Algorithm-Based Receptor Ligand: A Genetic Algorithm-Guided Generative Model to Boost the Novelty and Drug-Likeness of Molecules in a Sampling Chemical Space. 1213-1228 - Juan F. Avellaneda-Tamayo, Ana L. Chávez-Hernández, Diana L. Prado-Romero, José L. Medina-Franco:
Chemical Multiverse and Diversity of Food Chemicals. 1229-1244 - Peter Ertl:
Database of 4 Million Medicinal Chemistry-Relevant Ring Systems. 1245-1250 - Chen Cheng, Paul Beroza:
Shape-Aware Synthon Search (SASS) for Virtual Screening of Synthon-Based Chemical Spaces. 1251-1260 - Yang Wang, Yi Zhou, Ke Du:
Enumeration, Nomenclature, and Stability Rules of Carbon Nanobelts. 1261-1276 - Andrew S. Lee, Sarah Elliott, Hassan Harb, Logan T. Ward, Ian T. Foster, Larry A. Curtiss, Rajeev S. Assary:
Emin: A First-Principles Thermochemical Descriptor for Predicting Molecular Synthesizability. 1277-1289 - Connor M. Davel, Timotej Bernat, Jeffrey R. Wagner, Michael R. Shirts:
Parameterization of General Organic Polymers within the Open Force Field Framework. 1290-1305 - José E. González, Rafael Besse, Matheus P. Lima, Juarez L. F. Da Silva:
Decoding Van der Waals Impact on Chirality Transfer in Perovskite Structures: Density Functional Theory Insights. 1306-1318 - Xiaojie Jin, Min Zhang, Beibei Fu, Mi Li, Jingyi Yang, Zhiming Zhang, Chenghao Li, Huijuan Zhang, Haibo Wu, Weiwei Xue, Yongqi Liu:
Structure-Based Discovery of the SARS-CoV-2 Main Protease Noncovalent Inhibitors from Traditional Chinese Medicine. 1319-1330 - Colin L. Welsh, Lalima K. Madan:
Allostery in Protein Tyrosine Phosphatases is Enabled by Divergent Dynamics. 1331-1346 - Akhil Kumar, Manisha Sharma, Harshwardhan H. Katkar:
Peripheral Linker Mediates Acyl Carrier Protein's Recognition of Dehydratase and Stabilizes Type-I Mycobacterium tuberculosis Fatty Acid Synthase. 1347-1360 - Imane Euldji, Widad Benmouloud, Kamil Paduszynski, Cherif Si-Moussa, Othmane Benkortbi:
Hybrid Improved Grey Wolf Support Vector Regression Algorithm for Modeling Solubilities of APIs in Pure Ionic Liquids: σ-Profile Descriptors. 1361-1376 - Mateusz Lesniewski, Maciej Pyrka, Cezary Czaplewski, Nguyen Truong Co, Yida Jiang, Zhou Gong, Chun Tang, Adam Liwo:
Assessment of Two Restraint Potentials for Coarse-Grained Chemical-Cross-Link-Assisted Modeling of Protein Structures. 1377-1393 - Ming Zhang, Chao Gong, Fang Ge, Dong-Jun Yu:
FCMSTrans: Accurate Prediction of Disease-Associated nsSNPs by Utilizing Multiscale Convolution and Deep Feature Combination within a Transformer Framework. 1394-1406 - Zihao Yan, Fang Ge, Yan Liu, Yumeng Zhang, Fuyi Li, Jiangning Song, Dong-Jun Yu:
TransEFVP: A Two-Stage Approach for the Prediction of Human Pathogenic Variants Based on Protein Sequence Embedding Fusion. 1407-1418
Volume 64, Number 5, March 2024
- Issue Editorial Masthead.
- Issue Publication Information.
- Marjolein T. Oostrom, Sean M. Colby, Thomas O. Metz:
DEIMoS GUI: An Open-Source User Interface for a High-Dimensional Mass Spectrometry Data Processing Tool. 1419-1424 - Ewelina Jamrozik, Marek Smieja, Sabina Podlewska:
ADMET-PrInt: Evaluation of ADMET Properties: Prediction and Interpretation. 1425-1432 - Gao Tu, Tingting Fu, Guoxun Zheng, Binbin Xu, Rongpei Gou, Ding Luo, Panpan Wang, Weiwei Xue:
Computational Chemistry in Structure-Based Solute Carrier Transporter Drug Design: Recent Advances and Future Perspectives. 1433-1455 - Yunjiang Zhang, Shuyuan Li, Kong Meng, Shaorui Sun:
Machine Learning for Sequence and Structure-Based Protein-Ligand Interaction Prediction. 1456-1472 - Juliette Martin:
AlphaFold2 Predicts Whether Proteins Interact Amidst Confounding Structural Compatibility. 1473-1480 - Francesc Sabanés Zariquiey, Raimondas Galvelis, Emilio Gallicchio, John D. Chodera, Thomas E. Markland, Gianni De Fabritiis:
Enhancing Protein-Ligand Binding Affinity Predictions Using Neural Network Potentials. 1481-1485 - Son Gyo Jung, Guwon Jung, Jacqueline M. Cole:
Automatic Prediction of Peak Optical Absorption Wavelengths in Molecules Using Convolutional Neural Networks. 1486-1501 - Xinhui Li, Yurong Qian, Yue Hu, Jiaying Chen, Haitao Yue, Lei Deng:
MSF-PFP: A Novel Multisource Feature Fusion Model for Protein Function Prediction. 1502-1511 - Fernando Garcia-Escobar, Toshiaki Taniike, Keisuke Takahashi:
MonteCat: A Basin-Hopping-Inspired Catalyst Descriptor Search Algorithm for Machine Learning Models. 1512-1521 - Sung Wook Moon, Seung Kyu Min:
Gaussian Process Regression-Based Near-Infrared d-Luciferin Analogue Design Using Mutation-Controlled Graph-Based Genetic Algorithm. 1522-1532 - Pattipong Wisanpitayakorn, Sitanan Sartyoungkul, Alongkorn Kurilung, Yongyut Sirivatanauksorn, Wonnop Visessanguan, Nuankanya Sathirapongsasuti, Sakda Khoomrung:
Accurate Prediction of Ion Mobility Collision Cross-Section Using Ion's Polarizability and Molecular Mass with Limited Data. 1533-1542 - Xiaohe Xu, Weijie Han, Xiangzhen Ning, Chengdong Zang, Chengcheng Xu, Chen Zeng, Chengtao Pu, Yanmin Zhang, Yadong Chen, Haichun Liu:
Constructing Innovative Covalent and Noncovalent Compound Libraries: Insights from 3D Protein-Ligand Interactions. 1543-1559 - Gregory A. Landrum, Sereina Riniker:
Combining IC50 or Ki Values from Different Sources Is a Source of Significant Noise. 1560-1567 - Hatem Helal, Jesun Firoz, Jenna A. Bilbrey, Henry Sprueill, Kristina M. Herman, Mario Michael Krell, Tom Murray, Manuel Lopez Roldan, Mike Kraus, Ang Li, Payel Das, Sotiris S. Xantheas, Sutanay Choudhury:
Acceleration of Graph Neural Network-Based Prediction Models in Chemistry via Co-Design Optimization on Intelligence Processing Units. 1568-1580 - Camila M. Clemente, Juan M. Prieto, Marcelo A. Marti:
Unlocking Precision Docking for Metalloproteins. 1581-1592 - Giada Ciardullo, Angela Parise, Mario Prejanò, Tiziana Marino:
Viral RNA Replication Suppression of SARS-CoV-2: Atomistic Insights into Inhibition Mechanisms of RdRp Machinery by ddhCTP. 1593-1604 - Jochem Nelen, Miguel Carmena-Bargueño, Carlos Martinez-Cortes, Alejandro Rodríguez-Martínez, José Manuel Villalgordo-Soto, Horacio Pérez Sánchez:
ESSENCE-Dock: A Consensus-Based Approach to Enhance Virtual Screening Enrichment in Drug Discovery. 1605-1614 - Tien-Sheng Tseng, Chao-Chang Lee, Po-Juei Chen, Chiu-Yuen Lin, Wang-Chuan Chen, Yu-Ching Lee, Jiun-Han Lin, Kaun-Wen Chen, Keng-Chang Tsai:
Structure-Guided Discovery of PD-1/PD-L1 Interaction Inhibitors: Peptide Design, Screening, and Optimization via Computation-Aided Phage Display Engineering. 1615-1627 - Dávid Zajacek, Adriána Dunárová, Lukás Bucinský, Marek Steklác:
Compromise in Docking Power of Liganded Crystal Structures of Mpro SARS-CoV-2 Surpasses 90% Success Rate. 1628-1643 - Hong Ha Nguyen, Jim Tufts, David D. L. Minh:
On Inactivation of the Coronavirus Main Protease. 1644-1656 - Nishank Raisinghani, Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao, Gennady Verkhivker:
AlphaFold2-Enabled Atomistic Modeling of Structure, Conformational Ensembles, and Binding Energetics of the SARS-CoV-2 Omicron BA.2.86 Spike Protein with ACE2 Host Receptor and Antibodies: Compensatory Functional Effects of Binding Hotspots in Modulating Mechanisms of Receptor Binding and Immune Escape. 1657-1681 - Giulia Cazzanelli, Andrea Dalle Vedove, Giovanni Spagnolli, Luca Terruzzi, Enrica Colasurdo, Alberto Boldrini, Alexandros Patsilinakos, Mattia Sturlese, Alessandro Grottesi, Emiliano Biasini, Alessandro Provenzani, Alessandro Quattrone, Graziano Lolli:
Pliability in the m6A-Binding Region Extends Druggability of YTH Domains. 1682-1690 - Sebastian Anila, Sergey A. Samsonov:
Benchmarking Water Models in Molecular Dynamics of Protein-Glycosaminoglycan Complexes. 1691-1703 - Kaylen R. Meeks, Juan Ji, Mykola V. Protopopov, Olga O. Tarkhanova, Yurii S. Moroz, John J. Tanner:
Novel Fragment Inhibitors of PYCR1 from Docking-Guided X-ray Crystallography. 1704-1718 - Kun Wang, Ben Cao, Tao Ma, Yunzhu Zhao, Yanfen Zheng, Bin Wang, Shihua Zhou, Qiang Zhang:
Storing Images in DNA via base128 Encoding. 1719-1729 - Romanos Fasoulis, Maurício Menegatti Rigo, Gregory Lizée, Dinler A. Antunes, Lydia E. Kavraki:
APE-Gen2.0: Expanding Rapid Class I Peptide-Major Histocompatibility Complex Modeling to Post-Translational Modifications and Noncanonical Peptide Geometries. 1730-1750 - Zuojun Yang, Yuhan Wu, Hao Liu, Li He, Xiaoyuan Deng:
AMYGNN: A Graph Convolutional Neural Network-Based Approach for Predicting Amyloid Formation from Polypeptides. 1751-1762 - Nutaya Pravalphruekul, Maytus Piriyajitakonkij, Phond Phunchongharn, Supanida Piyayotai:
Correction to "De Novo Design of Molecules with Multiaction Potential from Differential Gene Expression using Variational Autoencoder". 1763
Volume 64, Number 6, 2024
- Marta Pasquini, Marco Stenta:
LinChemIn: Route Arithmetic─Operations on Digital Synthetic Routes. 1765-1771 - Yulei Wang, Yuxiang Wang:
HBCalculator: A Tool for Hydrogen Bond Distribution Calculations in Molecular Dynamics Simulations. 1772-1777 - Kuo-Hao Lee, Lei Shi:
Unraveling Activation-Related Rearrangements and Intrinsic Divergence from Ligand-Specific Conformational Changes of the Dopamine D3 and D2 Receptors. 1778-1793 - Yidan Tang, Rocco Moretti, Jens Meiler:
Recent Advances in Automated Structure-Based De Novo Drug Design. 1794-1805 - Uddeshya Pandey, Sasi M. Behara, Siddhant Sharma, Rachit S. Patil, Souparnika Nambiar, Debasish Koner, Hussain Bhukya:
DeePNAP: A Deep Learning Method to Predict Protein-Nucleic Acid Binding Affinity from Their Sequences. 1806-1815 - Tuan Vinh, Loc Nguyen, Quang H. Trinh, Thanh-Hoang Nguyen-Vo, Binh P. Nguyen:
Predicting Cardiotoxicity of Molecules Using Attention-Based Graph Neural Networks. 1816-1827 - Hugo Rossignol, Michail Minotakis, Matteo Cobelli, Stefano Sanvito:
Machine-Learning-Assisted Construction of Ternary Convex Hull Diagrams. 1828-1840 - Yendrek Velásquez-López, Andrea Ruiz-Escudero, Sonia Arrasate, Humberto González Díaz:
Implementation of IFPTML Computational Models in Drug Discovery Against Flaviviridae Family. 1841-1852 - Eleftherios Christofi, Petra Bacová, Vagelis Harmandaris:
Physics-Informed Deep Learning Approach for Reintroducing Atomic Detail in Coarse-Grained Configurations of Multiple Poly(lactic acid) Stereoisomers. 1853-1867 - Javad Tayebi, Bagher Babaali:
EKGDR: An End-to-End Knowledge Graph-Based Method for Computational Drug Repurposing. 1868-1881 - Zhonglin Cao, Simone Sciabola, Ye Wang:
Large-Scale Pretraining Improves Sample Efficiency of Active Learning-Based Virtual Screening. 1882-1891 - Ding Luo, Dandan Liu, Xiaoyang Qu, Lina Dong, Binju Wang:
Enhancing Generalizability in Protein-Ligand Binding Affinity Prediction with Multimodal Contrastive Learning. 1892-1906 - Derek P. Metcalf, Zachary L. Glick, Andrea Bortolato, Andy Jiang, Daniel L. Cheney, C. David Sherrill:
Directional ΔG Neural Network (DrΔG-Net): A Modular Neural Network Approach to Binding Free Energy Prediction. 1907-1918 - Vadim Korolev, Artem Mitrofanov:
Coarse-Grained Crystal Graph Neural Networks for Reticular Materials Design. 1919-1931 - Philipe Oliveira Fernandes, Anna Letícia Teotonio Dias, Valtair Severino dos Santos Júnior, Mateus Sá Magalhães Serafim, Yamara Viana Sousa, Gustavo Claro Monteiro, Isabel Duarte Coutinho, Marilia Valli, Marina Mol Sena Andrade Verzola, Flaviano Melo Ottoni, Rodrigo Maia de Pádua, Fernando Bombarda Oda, André Gustavo dos Santos, Adriano Defini Andricopulo, Vanderlan da Silva Bolzani, Bruno Eduardo Fernandes Mota, Ricardo José Alves, Renata Barbosa de Oliveira, Thales Kronenberger, Vinicius Gonçalves Maltarollo:
Machine Learning-Based Virtual Screening of Antibacterial Agents against Methicillin-Susceptible and Resistant Staphylococcus aureus. 1932-1944 - Jiancong Xie, Yi Wang, Jiahua Rao, Shuangjia Zheng, Yuedong Yang:
Self-Supervised Contrastive Molecular Representation Learning with a Chemical Synthesis Knowledge Graph. 1945-1954 - Rohan Gorantla, Alzbeta Kubincová, Benjamin Suutari, Benjamin P. Cossins, Antonia S. J. S. Mey:
Benchmarking Active Learning Protocols for Ligand-Binding Affinity Prediction. 1955-1965 - Daniela Dolciami, Robert M. Ziolek, Daniel W. Davies, Michael Carter, N. Yi Mok, Richard Sherhod:
Exploiting Vector Pattern Diversity of Molecular Scaffolds for Cheminformatics Tasks in Drug Discovery. 1966-1974 - Mohammadamin Tavakoli, Ryan J. Miller, Mirana Angel, Michael A. Pfeiffer, Eugene S. Gutman, Aaron Mood, David Van Vranken, Pierre Baldi:
PMechDB: A Public Database of Elementary Polar Reaction Steps. 1975-1983 - Angel Jonathan Ruiz-Moreno, Raziel Cedillo-González, Luis Cordova-Bahena, Zhiqiang An, José L. Medina-Franco, Marco Velasco-Velázquez:
Consensus Pharmacophore Strategy For Identifying Novel SARS-Cov-2 Mpro Inhibitors from Large Chemical Libraries. 1984-1995 - Szymon Zdybel, Anita Sosnowska, Dominika Kowalska, Julia Sommer, Beate Conrady, Patrick Mester, Maciej Gromelski, Tomasz Puzyn:
Hybrid Machine Learning and Experimental Studies of Antiviral Potential of Ionic Liquids against P100, MS2, and Phi6. 1996-2007 - Justin Lübbers, Uta F. Lessel, Matthias Rarey:
Enhanced Calculation of Property Distributions in Chemical Fragment Spaces. 2008-2020 - Farag E. S. Mosa, Sara Alrawashdeh, Ayman O. S. El-Kadi, Khaled H. Barakat:
Investigating the Aryl Hydrocarbon Receptor Agonist/Antagonist Conformational Switch Using Well-Tempered Metadynamics Simulations. 2021-2034 - Shawn C. C. Hsueh, Mark Nijland, Adekunle Aina, Steven S. Plotkin:
Cyclization Scaffolding for Improved Vaccine Immunogen Stability: Application to Tau Protein in Alzheimer's Disease. 2035-2044 - Jacqueline C. Calderón, Passainte Ibrahim, Dorothea Gobbo, Francesco Luigi Gervasio, Timothy Clark:
Determinants of Neutral Antagonism and Inverse Agonism in the β2-Adrenergic Receptor. 2045-2057 - Wan Wei, Lloyd Wei Tat Tang, Ravi Kumar Verma, Hao Fan, Eric Chun Yong Chan:
Probe Substrate Dependencies in CYP3A4 Allosteric Inhibition: A Novel Molecular Mechanism Involving F-F′ Loop Perturbations. 2058-2067 - Amit Kumar, Harish Vashisth:
Quantitative Assessment of Energetic Contributions of Residues in a SARS-CoV-2 Viral Enzyme/Nanobody Interface. 2068-2076 - Matic Broz, Chris Oostenbrink, Urban Bren:
The Effect of Microwaves on Protein Structure: Molecular Dynamics Approach. 2077-2083 - Omeir Khan, George Jones, Maria Lazou, Diane Joseph-McCarthy, Dima Kozakov, Dmitri Beglov, Sandor Vajda:
Expanding FTMap for Fragment-Based Identification of Pharmacophore Regions in Ligand Binding Sites. 2084-2100 - Sree Ganesh Balasubramani, Kseniia Korchagina, Steven Schwartz:
Transition Path Sampling Study of Engineered Enzymes That Catalyze the Morita-Baylis-Hillman Reaction: Why Is Enzyme Design so Difficult? 2101-2111 - Huifeng Zhao, Dejun Jiang, Chao Shen, Jintu Zhang, Xujun Zhang, Xiaorui Wang, Dou Nie, Tingjun Hou, Yu Kang:
Comprehensive Evaluation of 10 Docking Programs on a Diverse Set of Protein-Cyclic Peptide Complexes. 2112-2124
Volume 64, Number 7, 2024
- Kenneth M. Merz Jr., Guo-Wei Wei, Feng Zhu:
Editorial: Machine Learning in Bio-cheminformatics. 2125-2128 - Zoe Cournia, Christophe Chipot:
Applications of Free-Energy Calculations to Biomolecular Processes. A Collection. 2129-2131 - Deep Kumar Kirtania:
ChatGPT Generated Content and Similarity Index in Chemistry. 2132-2135 - Andrea Mauri, Matteo Bertola:
AlvaBuilder: A Software for De Novo Molecular Design. 2136-2142 - Michele Roggia, Benito Natale, Giorgio Amendola, Salvatore Di Maro, Sandro Cosconati:
Streamlining Large Chemical Library Docking with Artificial Intelligence: the PyRMD2Dock Approach. 2143-2149 - Natalia Lapinska, Adam Paclawski, Jakub Szlek, Aleksander Mendyk:
SerotoninAI: Serotonergic System Focused, Artificial Intelligence-Based Application for Drug Discovery. 2150-2157 - Yuanyuan Zhang, Zengqian Deng, Xiaoyu Xu, Yinfei Feng, Junliang Shang:
Application of Artificial Intelligence in Drug-Drug Interactions Prediction: A Review. 2158-2173 - Chao Pang, Jianbo Qiao, Xiangxiang Zeng, Quan Zou, Leyi Wei:
Deep Generative Models in De Novo Drug Molecule Generation. 2174-2194 - Benjamin Bouvier:
Substituted Oligosaccharides as Protein Mimics: Deep Learning Free Energy Landscapes. 2195-2204 - Xiangying Zhang, Haotian Gao, Haojie Wang, Zhihang Chen, Zhe Zhang, Xinchong Chen, Yan Li, Yifei Qi, Renxiao Wang:
PLANET: A Multi-objective Graph Neural Network Model for Protein-Ligand Binding Affinity Prediction. 2205-2220 - Xiaoyi Li, Wenyan Qu, Jing Yan, Jianjun Tan:
RPI-EDLCN: An Ensemble Deep Learning Framework Based on Capsule Network for ncRNA-Protein Interaction Prediction. 2221-2235 - Tingzhong Tian, Shuya Li, Meng Fang, Dan Zhao, Jianyang Zeng:
MolSHAP: Interpreting Quantitative Structure-Activity Relationships Using Shapley Values of R-Groups. 2236-2249 - José Ferraz-Caetano, Filipe Teixeira, Dthenifer Cordeiro Santana:
Explainable Supervised Machine Learning Model To Predict Solvation Gibbs Energy. 2250-2262 - Xiaoyang Qu, Lina Dong, Ding Luo, Yubing Si, Binju Wang:
Water Network-Augmented Two-State Model for Protein-Ligand Binding Affinity Prediction. 2263-2274 - Miriana Di Stefano, Salvatore Galati, Lisa Piazza, Carlotta Granchi, Simone Mancini, Filippo Fratini, Marco Macchia, Giulio Poli, Tiziano Tuccinardi:
VenomPred 2.0: A Novel In Silico Platform for an Extended and Human Interpretable Toxicological Profiling of Small Molecules. 2275-2289 - Zheng Fang, Zhongqi Wu, Xinbo Wu, Shixin Chen, Xing Wang, Saurabh Umrao, Abhisek Dwivedy:
APIPred: An XGBoost-Based Method for Predicting Aptamer-Protein Interactions. 2290-2301 - Ying Zhou, Ting Qi, Min Pan, Jing Tu, Xiangwei Zhao, Qinyu Ge, Zuhong Lu:
Deep-Cloud: A Deep Neural Network-Based Approach for Analyzing Differentially Expressed Genes of RNA-seq Data. 2302-2310 - Aaron R. Flanagan, Frank G. Glavin:
A Comparative Analysis of Data Synthesis Techniques to Improve Classification Accuracy of Raman Spectroscopy Data. 2311-2322 - Ghaith Mqawass, Petr Popov:
graphLambda: Fusion Graph Neural Networks for Binding Affinity Prediction. 2323-2330 - Wouter Heyndrickx, Lewis H. Mervin, Tobias Morawietz, Noé Sturm, Lukas Friedrich, Adam Zalewski, Anastasia Pentina, Lina Humbeck, Martijn Oldenhof, Ritsuya Niwayama, Peter Schmidtke, Nikolas Fechner, Jaak Simm, Adam Arany, Nicolas Drizard, Rama Jabal, Arina Afanasyeva, Regis Loeb, Shlok Verma, Simon Harnqvist, Matthew Holmes, Balazs Pejo, Maria Telenczuk, Nicholas Holway, Arne Dieckmann, Nicola Rieke, Friederike Zumsande, Djork-Arné Clevert, Michael Krug, Christopher N. Luscombe, Darren V. S. Green, Peter Ertl, Peter Antal, David Marcus, Nicolas Do Huu, Hideyoshi Fuji, Stephen D. Pickett, Gergely Ács, Eric Boniface, Bernd Beck, Yax Sun, Arnaud Gohier, Friedrich Rippmann, Ola Engkvist, Andreas H. Göller, Yves Moreau, Mathieu N. Galtier, Ansgar Schuffenhauer, Hugo Ceulemans:
MELLODDY: Cross-pharma Federated Learning at Unprecedented Scale Unlocks Benefits in QSAR without Compromising Proprietary Information. 2331-2344 - Yuki Matsukiyo, Chikashige Yamanaka, Yoshihiro Yamanishi:
De Novo Generation of Chemical Structures of Inhibitor and Activator Candidates for Therapeutic Target Proteins by a Transformer-Based Variational Autoencoder and Bayesian Optimization. 2345-2355 - Gianmattia Sgueglia, Michail D. Vrettas, Marco Chino, Alfonso De Simone, Angela Lombardi:
MetalHawk: Enhanced Classification of Metal Coordination Geometries by Artificial Neural Networks. 2356-2367 - Ewerton Cristhian Lima de Oliveira, Hannah Hirmz, Evelien Wynendaele, Juliana Auzier Seixas Feio, Igor Matheus Souza Moreira, Kauê Santana da Costa, Anderson H. Lima, Bart De Spiegeleer, Claudomiro de Souza de Sales Junior:
BrainPepPass: A Framework Based on Supervised Dimensionality Reduction for Predicting Blood-Brain Barrier-Penetrating Peptides. 2368-2382 - Hongle An, Xuyang Liu, Wensheng Cai, Xueguang Shao:
Explainable Graph Neural Networks with Data Augmentation for Predicting pKa of C-H Acids. 2383-2392 - Changjiang Li, Quan Zou, Cangzhi Jia, Jia Zheng:
AMPpred-MFA: An Interpretable Antimicrobial Peptide Predictor with a Stacking Architecture, Multiple Features, and Multihead Attention. 2393-2404 - Sean Cottrell, Rui Wang, Guo-Wei Wei:
PLPCA: Persistent Laplacian-Enhanced PCA for Microarray Data Analysis. 2405-2420 - Samuel Goldman, Jiayi Xin, Joules Provenzano, Connor W. Coley:
MIST-CF: Chemical Formula Inference from Tandem Mass Spectra. 2421-2431 - Hyeongwoo Kim, Kyunghoon Lee, Chansu Kim, Jaechang Lim, Woo Youn Kim:
DFRscore: Deep Learning-Based Scoring of Synthetic Complexity with Drug-Focused Retrosynthetic Analysis for High-Throughput Virtual Screening. 2432-2444 - Tzu-Hsien Yang, Jhih-Cheng Chen, Yuan-Han Lee, Shang-Yi Lu, Sheng-Hang Wu, Fang-Yuan Chang, Yan-Cheng Huang, Mei-Hsien Lee, Yan-Yuan Tseng, Wei-Sheng Wu:
Identifying Human miRNA Target Sites via Learning the Interaction Patterns between miRNA and mRNA Segments. 2445-2453 - Xuelian Li, Cheng Shen, Hui Zhu, Yujian Yang, Qing Wang, Jincai Yang, Niu Huang:
A High-Quality Data Set of Protein-Ligand Binding Interactions Via Comparative Complex Structure Modeling. 2454-2466 - Nieves C. Comelli, Patricia A. Diez, María R. Rodríguez, Gabriel O. Denett, Tamara E. López, Daniela M. Bracamonte, Erlinda V. Ortiz, Diego A. Sampietro, Pablo R. Duchowicz:
Excito-repellent and Pesticide-Likeness Properties of Essential Oils on Carpophilus dimidiatus (Fabricius) (Nitidulidae) and Oryzaephilus mercator (L.) (Silvanidae). 2467-2487 - Michael Brocidiacono, Paul G. Francoeur, Rishal Aggarwal, Konstantin I. Popov, David Ryan Koes, Alexander Tropsha:
BigBind: Learning from Nonstructural Data for Structure-Based Virtual Screening. 2488-2495 - Rohan Gorantla, Alzbeta Kubincová, Andrea Y. Weiße, Antonia S. J. S. Mey:
From Proteins to Ligands: Decoding Deep Learning Methods for Binding Affinity Prediction. 2496-2507 - Chaoshu Duan, Xuyang Liu, Wensheng Cai, Xueguang Shao:
Interpretable Perturbator for Variable Selection in near-Infrared Spectral Analysis. 2508-2514 - Issar Arab, Kristof Egghe, Kris Laukens, Ke Chen, Khaled H. Barakat, Wout Bittremieux:
Benchmarking of Small Molecule Feature Representations for hERG, Nav1.5, and Cav1.2 Cardiotoxicity Prediction. 2515-2527 - Zhaoyang Chen, Le Zhang, Pei Zhang, Huizhu Guo, Ruiqiu Zhang, Ling Li, Xiao Li:
Prediction of Cytochrome P450 Inhibition Using a Deep Learning Approach and Substructure Pattern Recognition. 2528-2538 - Emma Svensson, Pieter-Jan Hoedt, Sepp Hochreiter, Günter Klambauer:
HyperPCM: Robust Task-Conditioned Modeling of Drug-Target Interactions. 2539-2553 - Junjie Xie, Sheng Chen, Jinping Lei, Yuedong Yang:
DiffDec: Structure-Aware Scaffold Decoration with an End-to-End Diffusion Model. 2554-2564 - Henrique Barbosa, Gabriel Zarzana Espinoza, Maiara Amaral, Erica Valadares de Castro Levatti, Mariana Babberg Abiuzi, Gabriel Corrêa Veríssimo, Philipe de Oliveira Fernandes, Vinicius Gonçalves Maltarollo, Andre Gustavo Tempone, Káthia Maria Honório, João Henrique Ghilardi Lago:
Andrographolide: A Diterpenoid from Cymbopogon schoenanthus Identified as a New Hit Compound against Trypanosoma cruzi Using Machine Learning and Experimental Approaches. 2565-2576 - Fatemeh Rafiei, Hojjat Zeraati, Karim Abbasi, Parvin Razzaghi, Jahan B. Ghasemi, Mahboubeh Parsaeian, Ali Masoudi-Nejad:
CFSSynergy: Combining Feature-Based and Similarity-Based Methods for Drug Synergy Prediction. 2577-2585 - Katarzyna Kapuscinska, Zofia Dukala, Mekhola Doha, Eman Ansari, Jimin Wang, Gary W. Brudvig, Bernand Brooks, Muhamed Amin:
Bridging the Coordination Chemistry of Small Compounds and Metalloproteins Using Machine Learning. 2586-2593 - Andreas Zamanos, George Ioannakis, Ioannis Z. Emiris:
HydraProt: A New Deep Learning Tool for Fast and Accurate Prediction of Water Molecule Positions for Protein Structures. 2594-2611 - Egor Marin, Margarita Kovaleva, Maria Kadukova, Khalid Mustafin, Polina Khorn, Andrey Rogachev, Alexey Mishin, Albert Guskov, Valentin Borshchevskiy:
Regression-Based Active Learning for Accessible Acceleration of Ultra-Large Library Docking. 2612-2623 - Thomas M. Whitehead, Joel Strickland, Gareth John Conduit, Alexandre Borrel, Daniel Mucs, Irene Baskerville-Abraham:
Quantifying the Benefits of Imputation over QSAR Methods in Toxicology Data Modeling. 2624-2636 - Zachary Smith, Michael Strobel, Bodhi P. Vani, Pratyush Tiwary:
Graph Attention Site Prediction (GrASP): Identifying Druggable Binding Sites Using Graph Neural Networks with Attention. 2637-2644 - Linwei Sai, Li Fu, Jijun Zhao:
Predicting Binding Energies and Electronic Properties of Boron Nitride Fullerenes Using a Graph Convolutional Network. 2645-2653 - Xin Feng, Zhansen Ma, Cuinan Yu, Ruihao Xin:
MRNDR: Multihead Attention-Based Recommendation Network for Drug Repurposing. 2654-2669 - Yi He, Kaifeng Liu, Xiangyu Yu, Hengzheng Yang, Weiwei Han:
Building a Kokumi Database and Machine Learning-Based Prediction: A Systematic Computational Study on Kokumi Analysis. 2670-2680 - Niccolo Alberto Elia Venanzi, Andrea Basciu, Attilio Vittorio Vargiu, Alexandros Kiparissides, Paul A. Dalby, Duygu Dikicioglu:
Machine Learning Integrating Protein Structure, Sequence, and Dynamics to Predict the Enzyme Activity of Bovine Enterokinase Variants. 2681-2694 - William J. Godinez, Vladimir Trifonov, Bin Fang, Guray Kuzu, Luying Pei, W. Armand Guiguemde, Eric J. Martin, Frederick J. King, Jeremy L. Jenkins, Peter Skewes-Cox:
Compound Activity Prediction with Dose-Dependent Transcriptomic Profiles and Deep Learning. 2695-2704 - Subhojit Paul, Kaushika Olymon, Gustavo Sganzerla Martinez, Sharmilee Sarkar, Venkata Rajesh Yella, Aditya Kumar:
MLDSPP: Bacterial Promoter Prediction Tool Using DNA Structural Properties with Machine Learning and Explainable AI. 2705-2719 - Wei Zhang, Minjie Mou, Wei Hu, Mingkun Lu, Hanyu Zhang, Hongning Zhang, Yongchao Luo, Hongquan Xu, Lin Tao, Haibin Dai, Jianqing Gao, Feng Zhu:
MOINER: A Novel Multiomics Early Integration Framework for Biomedical Classification and Biomarker Discovery. 2720-2732 - Jiashun Mao, Jianmin Wang, Amir Zeb, Kwang-Hwi Cho, Haiyan Jin, Jongwan Kim, Onju Lee, Yunyun Wang, Kyoung Tai No:
Transformer-Based Molecular Generative Model for Antiviral Drug Design. 2733-2745 - Tong Xie, Yuwei Wan, Haoran Wang, Ina Østrøm, Shaozhou Wang, Mingrui He, Rong Deng, Xinyuan Wu, Clara Grazian, Chunyu Kit, Bram Hoex:
Opinion Mining by Convolutional Neural Networks for Maximizing Discoverability of Nanomaterials. 2746-2759 - Pawan Panwar, Quanpeng Yang, Ashlie Martini:
Temperature-Dependent Density and Viscosity Prediction for Hydrocarbons: Machine Learning and Molecular Dynamics Simulations. 2760-2774 - Pablo Rodríguez-Belenguer, Victor Mangas-Sanjuan, Emilio Soria-Olivas, Manuel Pastor:
Integrating Mechanistic and Toxicokinetic Information in Predictive Models of Cholestasis. 2775-2788 - Bodhi P. Vani, Akashnathan Aranganathan, Pratyush Tiwary:
Exploring Kinase Asp-Phe-Gly (DFG) Loop Conformational Stability with AlphaFold2-RAVE. 2789-2797 - Rui Wang, Zhecheng Zhou, Xiaonan Wu, Xin Jiang, Linlin Zhuo, Mingzhe Liu, Hao Li, Xiangzheng Fu, Xiaojun Yao:
An Effective Plant Small Secretory Peptide Recognition Model Based on Feature Correction Strategy. 2798-2806 - Xuetong Yang, Junru Jin, Ruheng Wang, Zhongshen Li, Yu Wang, Leyi Wei:
CACPP: A Contrastive Learning-Based Siamese Network to Identify Anticancer Peptides Based on Sequence Only. 2807-2816 - Tingjun Xu, Wenxing Gao, Lixin Zhu, Wanning Chen, Chaoqun Niu, Wenjing Yin, Liangxiao Ma, Xinyue Zhu, Yunchao Ling, Sheng Gao, Lei Liu, Na Jiao, Weiming Chen, Guoqing Zhang, Ruixin Zhu, Dingfeng Wu:
NAFLDkb: A Knowledge Base and Platform for Drug Development against Nonalcoholic Fatty Liver Disease. 2817-2828 - Yuta Hozumi, Kiyoto Aramis Tanemura, Guo-Wei Wei:
Preprocessing of Single Cell RNA Sequencing Data Using Correlated Clustering and Projection. 2829-2838 - Ruihao Xin, Fan Zhang, Jiaxin Zheng, Yangyi Zhang, Cuinan Yu, Xin Feng:
SDBA: Score Domain-Based Attention for DNA N4-Methylcytosine Site Prediction from Multiperspectives. 2839-2853 - Tianshuo Wang, Ruheng Wang, Leyi Wei:
AttenSyn: An Attention-Based Deep Graph Neural Network for Anticancer Synergistic Drug Combination Prediction. 2854-2862 - Jian He, Menglong Li, Jiangguo Qiu, Xuemei Pu, Yanzhi Guo:
HOPEXGB: A Consensual Model for Predicting miRNA/lncRNA-Disease Associations Using a Heterogeneous Disease-miRNA-lncRNA Information Network. 2863-2877 - Kai-Yang Zhong, Meng-Liang Wen, Fan-Fang Meng, Xin Li, Bei Jiang, Xin Zeng, Yi Li:
MMDTA: A Multimodal Deep Model for Drug-Target Affinity with a Hybrid Fusion Strategy. 2878-2888 - Haibin Li, Jun Meng, Zhaowei Wang, Youwei Tang, Shihao Xia, Yu Wang, Zhaojing Qin, Yushi Luan:
miPEPPred-FRL: A Novel Method for Predicting Plant MiRNA-Encoded Peptides Using Adaptive Feature Representation Learning. 2889-2900 - Shijie Xu, Akira Onoda:
Accurate and Fast Prediction of Intrinsically Disordered Protein by Multiple Protein Language Models and Ensemble Learning. 2901-2911 - Tao Wang, Wentao Wang, Xin Jiang, Jiaxing Mao, Linlin Zhuo, Mingzhe Liu, Xiangzheng Fu, Xiaojun Yao:
ML-NPI: Predicting Interactions between Noncoding RNA and Protein Based on Meta-Learning in a Large-Scale Dynamic Graph. 2912-2920 - Ziqiao Zhang, Yatao Bian, Ailin Xie, Pengju Han, Shuigeng Zhou:
Can Pretrained Models Really Learn Better Molecular Representations for AI-Aided Drug Discovery? 2921-2930
Volume 64, Number 8, 2024
- Tarak Karmakar, Thereza A. Soares, Kenneth M. Merz Jr.:
Enhancing Coarse-Grained Models through Machine Learning. 2931-2932 - Zhitao Cai, Hao Peng, Shuo Sun, Jiahao He, Fangfang Luo, Yandong Huang:
DeepKa Web Server: High-Throughput Protein pKa Prediction. 2933-2940 - Keda Yang, Zewen Xie, Zhen Li, Xiaoliang Qian, Nannan Sun, Tao He, Zuodong Xu, Jing Jiang, Qi Mei, Jie Wang, Shugang Qu, Xiaoling Xu, Chaoxiang Chen, Bin Ju:
MolProphet: A One-Stop, General Purpose, and AI-Based Platform for the Early Stages of Drug Discovery. 2941-2947 - Babak A. Mahjour, Connor W. Coley:
RDCanon: A Python Package for Canonicalizing the Order of Tokens in SMARTS Queries. 2948-2954 - Yuheng Ding, Bo Qiang, Qixuan Chen, Yiqiao Liu, Liangren Zhang, Zhenming Liu:
Exploring Chemical Reaction Space with Machine Learning Models: Representation and Feature Perspective. 2955-2970 - Lorenza Pirona, Federico Ballabio, Mercedes Alfonso-Prieto, Riccardo Capelli:
Calcium-Driven In Silico Inactivation of a Human Olfactory Receptor. 2971-2978 - Damla Ovek, Ozlem Keskin, Attila Gürsoy:
ProInterVal: Validation of Protein-Protein Interfaces through Learned Interface Representations. 2979-2987 - David C. Williams, Neil Inala:
Physics-Informed Generative Model for Drug-like Molecule Conformers. 2988-3007 - Maxwell C. Venetos, Masha Elkin, Connor Delaney, John F. Hartwig, Kristin A. Persson:
Deconvolution and Analysis of the 1H NMR Spectra of Crude Reaction Mixtures. 3008-3020 - Annie M. Westerlund, Siva Manohar Koki, Supriya Kancharla, Alessandro Tibo, Lakshidaa Saigiridharan, Mikhail Kabeshov, Rocío Mercado, Samuel Genheden:
Do Chemformers Dream of Organic Matter? Evaluating a Transformer Model for Multistep Retrosynthesis. 3021-3033 - Hazem Mslati, Francesco Gentile, Mohit Pandey, Fuqiang Ban, Artem Cherkasov:
PROTACable Is an Integrative Computational Pipeline of 3-D Modeling and Deep Learning To Automate the De Novo Design of PROTACs. 3034-3046 - Zhihao Gu, Yong Yan, Hanwen Liu, Di Wu, Hequan Yao, Kejiang Lin, Xuanyi Li:
Discovery of Covalent Lead Compounds Targeting 3CL Protease with a Lateral Interactions Spiking Neural Network. 3047-3058 - Miguel Gallegos, Bienfait Kabuyaya Isamura, Paul L. A. Popelier, Ángel Martín Pendás:
An Unsupervised Machine Learning Approach for the Automatic Construction of Local Chemical Descriptors. 3059-3079 - Jianing Fan, Shao-Hua Shi, Hong Xiang, Li Fu, Yanjing Duan, Dong-Sheng Cao, Hongwei Lu:
Predicting Elimination of Small-Molecule Drug Half-Life in Pharmacokinetics Using Ensemble and Consensus Machine Learning Methods. 3080-3092 - Ida Rahu, Meelis Kull, Anneli Kruve:
Predicting the Activity of Unidentified Chemicals in Complementary Bioassays from the HRMS Data to Pinpoint Potential Endocrine Disruptors. 3093-3104 - Lei Song, Huimin Zhu, Kaili Wang, Min Li:
LGGA-MPP: Local Geometry-Guided Graph Attention for Molecular Property Prediction. 3105-3113 - Sebastian Schieferdecker, Florian Rottach, Esther Vock:
In Silico Prediction of Oral Acute Rodent Toxicity Using Consensus Machine Learning. 3114-3122 - Xiangwen Wang, Derek Quinn, Thomas S. Moody, Meilan Huang:
ALDELE: All-Purpose Deep Learning Toolkits for Predicting the Biocatalytic Activities of Enzymes. 3123-3139 - Hongni Jin, Kenneth M. Merz Jr.:
Modeling Zinc Complexes Using Neural Networks. 3140-3148 - Jiamin Chang, Xiaoyu Fan, Boxue Tian:
DeepP450: Predicting Human P450 Activities of Small Molecules by Integrating Pretrained Protein Language Model and Molecular Representation. 3149-3160 - Mustafa Kemal Ozalp, Patricia A. Vignaux, Ana C. Puhl, Thomas R. Lane, Fabio Urbina, Sean Ekins:
Sequential Contrastive and Deep Learning Models to Identify Selective Butyrylcholinesterase Inhibitors. 3161-3172 - Ramil I. Nugmanov:
PaCh (Packed Chemicals): Computationally Effective Binary Format for Chemical Structure Encoding. 3173-3179 - Martin Priessner, Richard J. Lewis, Magnus J. Johansson, Jonathan M. Goodman, Jon Paul Janet, Anna Tomberg:
HSQC Spectra Simulation and Matching for Molecular Identification. 3180-3191 - Maria José Tenorio, Miguel Á. González, Julia D. Magdaleno, Inmaculada Suárez, Baudilio Coto:
Viscosities and Densities of Binary and Ternary Mixtures of Aliphatic and Polyaromatic Hydrocarbons: Pyrene +1-Methylnaphthalene + Dodecane at T = (293.15 to 343.15) K. Experiment and Modeling. 3192-3204 - Taketomo Isazawa, Jacqueline M. Cole:
How Beneficial Is Pretraining on a Narrow Domain-Specific Corpus for Information Extraction about Photocatalytic Water Splitting? 3205-3212 - Daimon Sakaguchi, Hiroaki Gotoh:
Using Three-Dimensional Information to Predict and Interpret the Facial Selectivities of Nucleophilic Additions to Cyclic Ketones. 3213-3221 - Teng-Zhi Long, Dejun Jiang, Shao-Hua Shi, You-Chao Deng, Wen-Xuan Wang, Dong-Sheng Cao:
Enhancing Multi-species Liver Microsomal Stability Prediction through Artificial Intelligence. 3222-3236 - Shreya Bhattacharya, Priyadarshi Satpati:
Why Does the E1219V Mutation Expand T-Rich PAM Recognition in Cas9 from Streptococcus pyogenes? 3237-3247 - Didier Desmecht, Vincent Dubois:
Correlation of the Molecular Cross-Sectional Area of Organic Monofunctional Compounds with Topological Descriptors. 3248-3259 - Shivam Parashar, Alexander V. Neimark:
Pore Structure Compartmentalization for Advanced Characterization of Metal-Organic Framework Materials. 3260-3268 - Luis Macaya, Duván González, Esteban Vöhringer-Martinez:
Nonbonded Force Field Parameters from MBIS Partitioning of the Molecular Electron Density Improve Binding Affinity Predictions of the T4-Lysozyme Double Mutant. 3269-3277 - Felipe L. Oliveira, Pierre M. Esteves:
pyCOFBuilder: A Python Package for Automated Creation of Covalent Organic Framework Models Based on the Reticular Approach. 3278-3289 - Valentin Milia, Nathalie Tarrat, Christophe Zanon, Juan Cortés, Mathias Rapacioli:
Exploring Molecular Energy Landscapes by Coupling the DFTB Potential with a Tree-Based Stochastic Algorithm: Investigation of the Conformational Diversity of Phthalates. 3290-3301 - Arkadiusz Leniak, Wojciech Pietrus, Rafal Kurczab:
From NMR to AI: Designing a Novel Chemical Representation to Enhance Machine Learning Predictions of Physicochemical Properties. 3302-3321 - Rodrigo A. Cormanich, Gabriel D. da Silva:
Autobench V1.0: Benchmarking Automation for Electronic Structure Calculations. 3322-3331 - Joel Graef, Christiane Ehrt, Thorben Reim, Matthias Rarey:
Database-Driven Identification of Structurally Similar Protein-Protein Interfaces. 3332-3349 - Ander Francisco Pereira, Leandro Martínez:
Helical Content Correlations and Hydration Structures of the Folding Ensemble of the B Domain of Protein A. 3350-3359 - Satyabrata Majumder, Giuseppe Deganutti, Ludovico Pipitò, Dwaipayan Chaudhuri, Joyeeta Datta, Kalyan Giri:
Computational Insights into the Conformational Dynamics of HIV-1 Vpr in a Lipid Bilayer for Ion Channel Modeling. 3360-3374 - Nicolas Chéron:
Binding Sites of Bicarbonate in Phosphoenolpyruvate Carboxylase. 3375-3385 - Yu Zou, Lulu Guan, Jingwang Tan, Bote Qi, Yunxiang Sun, Fengjuan Huang, Qingwen Zhang:
Molecular Insights into the Differential Effects of Acetylation on the Aggregation of Tau Microtubule-Binding Repeats. 3386-3399 - Ru-De Lin, Xiu Xing, Yuan Yu, Wen-Dian Li, Dan-Dan Chang, Fei-Yan Tao, Na Wang:
Theoretical Analysis of Selectivity Differences in Ketoreductases toward Aldehyde and Ketone Carbonyl Groups. 3400-3410 - Jiaojiao Wang, Ting Ren, Guohui Sun, Na Zhang, Lijiao Zhao, Rugang Zhong:
Mechanism of AGT-Mediated Repair of dG-dC Cross-Links in the Drug Resistance to Chloroethylnitrosoureas: Molecular Docking, MD Simulation, and ONIOM (QM/MM) Investigation. 3411-3429 - Filipe E. P. Rodrigues, Tamis Darbre, Miguel Machuqueiro:
High Charge Density in Peptide Dendrimers is Required to Destabilize Membranes: Insights into Endosome Evasion. 3430-3442 - Rafael Giordano Viegas, Ingrid B. S. Martins, Murilo Nogueira Sanches, Antonio B. Oliveira Junior, Juliana B. de Camargo, Fernando V. Paulovich, Vitor B. P. Leite:
ELViM: Exploring Biomolecular Energy Landscapes through Multidimensional Visualization. 3443-3450 - Yanjun Feng, Changda Gong, Jieyu Zhu, Guixia Liu, Yun Tang, Weihua Li:
Unraveling the Ligand-Binding Sites of CYP3A4 by Molecular Dynamics Simulations with Solvent Probes. 3451-3464 - Luis J. Walter, Patrick K. Quoika, Martin Zacharias:
Structure-Based Protein Assembly Simulations Including Various Binding Sites and Conformations. 3465-3476 - Riya Samanta, Xinhao Zhuang, Kristen M. Varney, David J. Weber, Silvina Matysiak:
Deciphering S100B Allosteric Signaling: The Role of a Peptide Target, TRTK-12, as an Ensemble Modulator. 3477-3487 - Angela M. Barragan, Kyle Ghaby, Matthew P. Pond, Benoît Roux:
Computational Investigation of the Covalent Inhibition Mechanism of Bruton's Tyrosine Kinase by Ibrutinib. 3488-3502 - Tian Hua Wang, Haiping Shao, Bingqiang Zhao, Hong Lin Zhai:
Molecular Insights into the Variability in Infection and Immune Evasion Capabilities of SARS-CoV-2 Variants: A Sequence and Structural Investigation of the RBD Domain. 3503-3523 - Tengyu Xie, Jing Huang:
Can Protein Structure Prediction Methods Capture Alternative Conformations of Membrane Transporters? 3524-3536 - Yi Zhang, Xuanzhao Li:
Empowering Graph Neural Networks with Block-Based Dual Adaptive Deep Adjustment for Drug Resistance-Related NcRNA Discovery. 3537-3547 - Lianci Tao, Tong Zhou, Zhixiang Wu, Fangrui Hu, Shuang Yang, Xiaotian Kong, Chunhua Li:
ESPDHot: An Effective Machine Learning-Based Approach for Predicting Protein-DNA Interaction Hotspots. 3548-3557 - Zhe Su, Yiying Tong, Guo-Wei Wei:
Hodge Decomposition of Single-Cell RNA Velocity. 3558-3568 - Ping Xuan, Siyuan Lu, Hui Cui, Shuai Wang, Toshiya Nakaguchi, Tiangang Zhang:
Learning Association Characteristics by Dynamic Hypergraph and Gated Convolution Enhanced Pairwise Attributes for Prediction of Disease-Related lncRNAs. 3569-3578 - Hongyan Chen, Dongxue Yan, Jie Sun, Meng Zhou:
Inference of Developmental Hierarchy and Functional States of Exhausted T Cells from Epigenetic Profiles with Deep Learning. 3579-3591 - Diego Moreno Martinez, Dominique Guillaumont, Philippe Guilbaud:
Addition to "Force Field Parameterization of Actinyl Molecular Cations Using the 12-6-4 Model". 3592
Volume 64, Number 9, 2024
- Sergey Gorelov, Anatoly Titov, Olga Tolicheva, Andrey Konevega, Alexey Shvetsov:
DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in Trajectories. 3593-3598 - Pengchao Zhang, Axel Tosello Gardini, Xuefei Xu, Michele Parrinello:
Intramolecular and Water Mediated Tautomerism of Solvated Glycine. 3599-3604 - Stefan Boresch:
On Analytical Corrections for Restraints in Absolute Binding Free Energy Calculations. 3605-3609 - Maksim Kuznetsov, Fedor Ryabov, Roman Schutski, Rim Shayakhmetov, Yen-Chu Lin, Alex Aliper, Daniil Polykovskiy:
COSMIC: Molecular Conformation Space Modeling in Internal Coordinates with an Adversarial Framework. 3610-3620 - Hajime Shimakawa, Akiko Kumada, Masahiro Sato:
Prevention of Leakage in Machine Learning Prediction for Polymer Composite Properties. 3621-3629 - Shukai Gu, Yuwei Yang, Yihao Zhao, Jiayue Qiu, Xiaorui Wang, Henry Hoi Yee Tong, Liwei Liu, Xiaozhe Wan, Huanxiang Liu, Tingjun Hou, Yu Kang:
Evaluation of AlphaFold2 Structures for Hit Identification across Multiple Scenarios. 3630-3639 - Da-zhou Li, Xin Xu, Jia-heng Pan, Wei Gao, Shi-rui Zhang:
Image2InChI: Automated Molecular Optical Image Recognition. 3640-3649 - Bingxin Zhou, Lirong Zheng, Banghao Wu, Yang Tan, Outongyi Lv, Kai Yi, Guisheng Fan, Liang Hong:
Protein Engineering with Lightweight Graph Denoising Neural Networks. 3650-3661 - Koichi Handa, Saki Yoshimura, Michiharu Kageyama, Takeshi Iijima:
Development of Novel Methods for QSAR Modeling by Machine Learning Repeatedly: A Case Study on Drug Distribution to Each Tissue. 3662-3669 - Moritz Walter, Samuel J. Webb, Valerie J. Gillet:
Interpreting Neural Network Models for Toxicity Prediction by Extracting Learned Chemical Features. 3670-3688 - Yu Pang, Yihao Chen, Mujie Lin, Yanhong Zhang, Jiquan Zhang, Ling Wang:
MMSyn: A New Multimodal Deep Learning Framework for Enhanced Prediction of Synergistic Drug Combinations. 3689-3705 - Yu Zhu, Jing Gu, Zhuoran Zhao, A. W. Edith Chan, Maria F. Mojica, Andrea M. Hujer, Robert A. Bonomo, Shozeb M. Haider:
Deciphering the Coevolutionary Dynamics of L2 β-Lactamases via Deep Learning. 3706-3717 - Shuang Wang, Dingming Liang, Jianmin Wang, Kaiyu Dong, Yunjing Zhang, Huicong Liang, Ximing Xu, Tao Song:
FraHMT: A Fragment-Oriented Heterogeneous Graph Molecular Generation Model for Target Proteins. 3718-3732 - Vincenzo Vigna, Tânia F. G. G. Cova, Sandra C. C. Nunes, A. A. C. C. Pais, Emilia Sicilia:
Machine Learning-Based Prediction of Reduction Potentials for PtIV Complexes. 3733-3743 - Haopeng Ai, Deyin Wu, Huihao Zhou, Jun Xu, Qiong Gu:
dMXP: A De Novo Small-Molecule 3D Structure Predictor with Graph Attention Networks. 3744-3755 - Tzu-Hsien Yang:
DEBFold: Computational Identification of RNA Secondary Structures for Sequences across Structural Families Using Deep Learning. 3756-3766 - Otávio L. Santana, Daniel G. Silva, Sidney R. Santana:
Solvate Suite: A Command-Line Interface for Molecular Simulations and Multiscale Microsolvation Modeling. 3767-3778 - Boyang Ni, Haoying Wang, Huda Kadhim Salem Khalaf, Vincent Blay, Douglas R. Houston:
AutoDock-SS: AutoDock for Multiconformational Ligand-Based Virtual Screening. 3779-3789 - Daniel S. Wigh, Joe Arrowsmith, Alexander Pomberger, Kobi C. Felton, Alexei A. Lapkin:
ORDerly: Data Sets and Benchmarks for Chemical Reaction Data. 3790-3798 - Marzieh Saeedimasine, Roja Rahmani, Alexander P. Lyubartsev:
Biomolecular Adsorption on Nanomaterials: Combining Molecular Simulations with Machine Learning. 3799-3811 - Pieter Buys Burger, Xiaohu Hu, Ilya Balabin, Morné Muller, Megan Stanley, Fourie Joubert, Thomas M. Kaiser:
FEP Augmentation as a Means to Solve Data Paucity Problems for Machine Learning in Chemical Biology. 3812-3825 - Rohan Chandraghatgi, Hai-Feng Ji, Gail L. Rosen, Bahrad A. Sokhansanj:
Streamlining Computational Fragment-Based Drug Discovery through Evolutionary Optimization Informed by Ligand-Based Virtual Prescreening. 3826-3840 - Sankar Maity, Somdev Pahari, Santanu Santra, Madhurima Jana:
Interfacial Glucose to Regulate Hydrated Lipid Bilayer Properties: Influence of Concentrations. 3841-3854 - Dulce C. Guzmán-Ocampo, Rodrigo Aguayo-Ortiz, Laura Dominguez:
Understanding the Modulatory Role of E2012 on the γ-Secretase-Substrate Interaction. 3855-3864 - David Ferro-Costas, Pedro A. Sánchez-Murcia, Antonio Fernández-Ramos:
Unraveling the Catalytic Mechanism of β-Cyclodextrin in the Vitamin D Formation. 3865-3873 - Lina Zhao, Yanjiao Wang, Yi Zhang, Hao Chen, Fude Sun:
Dynamic Simulations of Interaction of the PEG-DPPE Micelle-Encapsulated Short-Chain Ceramides with the Raft-Included Membrane. 3874-3883 - Masao Inoue, Toru Ekimoto, Tsutomu Yamane, Mitsunori Ikeguchi:
Computational Analysis of Activation of Dimerized Epidermal Growth Factor Receptor Kinase Using the String Method and Markov State Model. 3884-3895 - Zhengyue Zhang, Vojtech Mlýnský, Miroslav Krepl, Jirí Sponer, Petr Stadlbauer:
Mechanical Stability and Unfolding Pathways of Parallel Tetrameric G-Quadruplexes Probed by Pulling Simulations. 3896-3911 - Paige E. Bowling, Saswata Dasgupta, John M. Herbert:
Eliminating Imaginary Vibrational Frequencies in Quantum-Chemical Cluster Models of Enzymatic Active Sites. 3912-3922 - Krishnendu Sinha, Ipsita Basu, Zacharia Shah, Salim Shah, Suman Chakrabarty:
Leveraging Bidirectional Nature of Allostery To Inhibit Protein-Protein Interactions (PPIs): A Case Study of PCSK9-LDLR Interaction. 3923-3932 - Ying Zheng, Nianhang Chen, Zhongju Ji, Qiongyu Ye, Pingping Huang, Xiaodie Chen, Guanghong Cui, Lixin Duan, Fan Zhang:
Adjusting Catalytic Activity of β-Amyrin Synthase GgBAS by Utilizing the Plasticity Residues of an Active Site. 3933-3941 - Mueed Ur Rahman, Saira Bano, Xiaokun Hong, Ruo-Xu Gu, Hai-Feng Chen:
Early Aggregation Mechanism of SOD128-38 Based on Force Field Parameter of 5-Cyano-Tryptophan. 3942-3952 - Dhiman Ray, Sudip Das, Umberto Raucci:
Kinetic View of Enzyme Catalysis from Enhanced Sampling QM/MM Simulations. 3953-3958
Volume 64, Number 10, 2024
- Issue Editorial Masthead.
- Issue Publication Information.
- Kenneth M. Merz Jr., Yee-Siew Choong, Zoe Cournia, Olexandr Isayev, Thereza A. Soares, Guo-Wei Wei, Feng Zhu:
Editorial: Machine Learning in Materials Science. 3959-3960 - Petrina Kamya, Ivan V. Ozerov, Frank W. Pun, Kyle Tretina, Tatyana Fokina, Shan Chen, Vladimir Naumov, Xi Long, Sha Lin, Mikhail Korzinkin, Daniil Polykovskiy, Alex Aliper, Feng Ren, Alex Zhavoronkov:
PandaOmics: An AI-Driven Platform for Therapeutic Target and Biomarker Discovery. 3961-3969 - Yueqing Zhang, Zhihan Zhang, Dongliang Ke, Xiaolin Pan, Xingyu Wang, Xudong Xiao, Changge Ji:
FragGrow: A Web Server for Structure-Based Drug Design by Fragment Growing within Constraints. 3970-3976 - Zishuo Cheng, Mahesh Aitha, Caitlyn A. Thomas, Aidan Sturgill, Mitch Fairweather, Amy Hu, Christopher R. Bethel, Dann D. Rivera, Patricia Dranchak, Pei W. Thomas, Han Li, Qi Feng, Kaicheng Tao, Minshuai Song, Na Sun, Shuo Wang, Surendra Bikram Silwal, Richard C. Page, Walt Fast, Robert A. Bonomo, Maria Weese, Waldyn G. Martinez, James Inglese, Michael W. Crowder:
Machine Learning Models Identify Inhibitors of New Delhi Metallo-β-lactamase. 3977-3991 - Payam Kelich, Jaquesta Adams, Sanghwa Jeong, Nicole Navarro, Markita P. Landry, Lela Vukovic:
Predicting Serotonin Detection with DNA-Carbon Nanotube Sensors across Multiple Spectral Wavelengths. 3992-4001 - Ting Qi, Ying Zhou, Yuqi Sheng, Zhihui Li, Yuwei Yang, Quanjun Liu, Qinyu Ge:
Prediction of Transcription Factor Binding Sites on Cell-Free DNA Based on Deep Learning. 4002-4008 - Michael Backenköhler, Joschka Groß, Verena Wolf, Andrea Volkamer:
Guided Docking as a Data Generation Approach Facilitates Structure-Based Machine Learning on Kinases. 4009-4020 - Ronen Taub, Yonatan Savir:
SAF: Smart Aggregation Framework for Revealing Atoms Importance Rank and Improving Prediction Rates in Drug Discovery. 4021-4030 - Hosein Fooladi, Steffen Hirte, Johannes Kirchmair:
Quantifying the Hardness of Bioactivity Prediction Tasks for Transfer Learning. 4031-4046 - Juan S. Grassano, Ignacio Pickering, Adrian E. Roitberg, Mariano C. González Lebrero, Dario A. Estrin, Jonathan Alexis Semelak:
Assessment of Embedding Schemes in a Hybrid Machine Learning/Classical Potentials (ML/MM) Approach. 4047-4058 - Rongpei Gou, Jingyi Yang, Menghan Guo, Yingjun Chen, Weiwei Xue:
CNSMolGen: A Bidirectional Recurrent Neural Network-Based Generative Model for De Novo Central Nervous System Drug Design. 4059-4070 - Vishal Dey, Xia Ning:
Improving Anticancer Drug Selection and Prioritization via Neural Learning to Rank. 4071-4088 - Arghya Chakravorty, Azam Hussain, Luis F. Cervantes, Thanh T. Lai, Charles L. Brooks III:
Exploring the Limits of the Generalized CHARMM and AMBER Force Fields through Predictions of Hydration Free Energy of Small Molecules. 4089-4101 - Renxiu Song, Kaifeng Liu, Qizheng He, Fei He, Weiwei Han:
Exploring Bitter and Sweet: The Application of Large Language Models in Molecular Taste Prediction. 4102-4111 - Mehdi Sahihi, Pierre Fayon, Lionel Nauton, Florent Goujon, Julien Devémy, Alain Dequidt, Patrice Hauret, Patrice Malfreyt:
Probing Enzymatic PET Degradation: Molecular Dynamics Analysis of Cutinase Adsorption and Stability. 4112-4120 - Sonia Kumari, Masilamani Elizabeth Sobhia:
Targeting an Old Foe for Cancer: A Molecular Dynamics Perspective to Unravel the Specific Binding Nature of 2-Methoxy Estradiol to Human β-Tubulin Isotypes. 4121-4133 - José Luis Velázquez-Libera, Julio Caballero, Jans H. Alzate-Morales, Jose Javier Ruiz-Pernía, Iñaki Tuñón:
Understanding the Interactions of Ubiquitin-Specific Protease 7 with Its Substrates through Molecular Dynamics Simulations: Insights into the Role of Its C-Terminal Domains in Substrate Recognition. 4134-4148 - Rafael Giordano Viegas, Ingrid B. S. Martins, Vitor B. P. Leite:
Understanding the Energy Landscape of Intrinsically Disordered Protein Ensembles. 4149-4157 - Gert-Jan Bekker, Kanji Oshima, Mitsugu Araki, Yasushi Okuno, Narutoshi Kamiya:
Binding Mechanism between Platelet Glycoprotein and Cyclic Peptide Elucidated by McMD-Based Dynamic Docking. 4158-4167 - Wen-Hao Deng, Rong-Zhen Liao:
Cysteine Radical and Glutamate Collaboratively Enable C-H Bond Activation and C-N Bond Cleavage in a Glycyl Radical Enzyme HplG. 4168-4179 - Yu Du:
Binding Curve Viewer: Visualizing the Equilibrium and Kinetics of Protein-Ligand Binding and Competitive Binding. 4180-4192 - Farzin Sohraby, Ariane Nunes-Alves:
Characterization of the Bottlenecks and Pathways for Inhibitor Dissociation from [NiFe] Hydrogenase. 4193-4203 - Mateusz Rzycki, Dominik Drabik:
Multifaceted Activity of Fabimycin: Insights from Molecular Dynamics Studies on Bacterial Membrane Models. 4204-4217 - Pedro Ferreira, Rui P. P. Neves, Filipa P. Miranda, Ana V. Cunha, Remco W. A. Havenith, Maria João Ramos, Pedro Alexandrino Fernandes:
DszA Catalyzes C-S Bond Cleavage through N5-Hydroperoxyl Formation. 4218-4230 - Yazdan Maghsoud, Arkanil Roy, Emmett M. Leddin, G. Andrés Cisneros:
Effects of the Y432S Cancer-Associated Variant on the Reaction Mechanism of Human DNA Polymerase κ. 4231-4249 - Sunita Muduli, Soumyajit Karmakar, Sabyashachi Mishra:
Conformational Dynamics in Corynebacterium glutamicum Diaminopimelate Epimerase: Insights from Ligand Parameterization, Atomistic Simulation, and Markov State Modeling. 4250-4262 - Simona De Vita, Ester Colarusso, Maria Giovanna Chini, Giuseppe Bifulco, Gianluigi Lauro:
PharmaCore: The Automatic Generation of 3D Structure-Based Pharmacophore Models from Protein/Ligand Complexes. 4263-4276 - Jin Zhang, Xinhao Sun, Hongwei Zhao, Xu Zhou, Yiling Zhang, Feng Xie, Boyan Li, Guo Guo:
In Silico Design and Synthesis of Antifungal Peptides Guided by Quantitative Antifungal Activity. 4277-4285 - Ruslan Kotlyarov, Konstantinos Papachristos, Geoffrey P. F. Wood, Jonathan M. Goodman:
Leveraging Language Model Multitasking To Predict C-H Borylation Selectivity. 4286-4297 - Vinay Kumar, Arkaprava Banerjee, Kunal Roy:
Breaking the Barriers: Machine-Learning-Based c-RASAR Approach for Accurate Blood-Brain Barrier Permeability Prediction. 4298-4309 - Greneter Cordoves-Delgado, César R. García-Jacas:
Predicting Antimicrobial Peptides Using ESMFold-Predicted Structures and ESM-2-Based Amino Acid Features with Graph Deep Learning. 4310-4321 - Jujuan Zhuang, Xinru Huang, Shuhan Liu, Wanquan Gao, Rui Su, Kexin Feng:
MulTFBS: A Spatial-Temporal Network with Multichannels for Predicting Transcription Factor Binding Sites. 4322-4333 - Ning Cheng, Li Wang, Yiping Liu, Bosheng Song, Changsong Ding:
HANSynergy: Heterogeneous Graph Attention Network for Drug Synergy Prediction. 4334-4347 - Bao-Ming Feng, Yuan-Yuan Zhang, Xiao-Chen Zhou, Jin-Long Wang, Yinfei Feng:
MolLoG: A Molecular Level Interpretability Model Bridging Local to Global for Predicting Drug Target Interactions. 4348-4358 - Yue Luo, Lei Deng:
DPMGCDA: Deciphering circRNA-Drug Sensitivity Associations with Dual Perspective Learning and Path-Masked Graph Autoencoder. 4359-4372 - Sizhe Zhang, Xuecong Tian, Chen Chen, Ying Su, Wanhua Huang, Xiaoyi Lv, Cheng Chen, Hongyi Li:
AIGO-DTI: Predicting Drug-Target Interactions Based on Improved Drug Properties Combined with Adaptive Iterative Algorithms. 4373-4384 - Jun Zhao, Qinhai Ma, Baoyue Zhang, Pengfei Guo, Zhe Wang, Yi Liu, Minsi Meng, Ailin Liu, Zifeng Yang, Guanhua Du:
Correction to "Exploration of SARS-CoV-2 3CLpro Inhibitors by Virtual Screening Methods, FRET Detection, and CPE Assay". 4385-4386
Volume 64, Number 11, 2024
- James Wellnitz, Holli-Joi Martin, Mohammad Anwar Hossain, Marielle Rath, Colton Fox, Konstantin I. Popov, Timothy M. Willson, Eugene N. Muratov, Alexander Tropsha:
STOPLIGHT: A Hit Scoring Calculator. 4387-4391 - Kha-Dinh Luong, Ambuj K. Singh:
Application of Transformers in Cheminformatics. 4392-4409 - Siyuan Liu, Qi Yang, Long Zhang, Sanzhong Luo:
Accurate Protein pKa Prediction with Physical Organic Chemistry Guided 3D Protein Representation. 4410-4418 - Qin Xie, Andrew P. Horsfield:
Coordinate-Free and Low-Order Scaling Machine Learning Model for Atomic Partial Charge Prediction for Any Size of Molecules. 4419-4425 - Arnab Jana, Sam Shepherd, Yair Litman, David M. Wilkins:
Learning Electronic Polarizations in Aqueous Systems. 4426-4435 - Floriane Eshak, Léo Pion, Pauline Scholler, Damien Nevoltris, Patrick Chames, Philippe Rondard, Jean-Philippe Pin, Francine C. Acher, Anne Goupil-Lamy:
Epitope Identification of an mGlu5 Receptor Nanobody Using Physics-Based Molecular Modeling and Deep Learning Techniques. 4436-4461 - Brunno A. Salvatti, Marcelo A. Chagas, Phillipe O. Fernandes, Yan F. X. Ladeira, Aline S. Bozzi, Veronica S. Valadares, Ana Paula Valente, Amanda S. de Miranda, Willian R. Rocha, Vinicius Gonçalves Maltarollo, Adolfo H. Moraes:
Understanding the Enzyme (S)-Norcoclaurine Synthase Promiscuity to Aldehydes and Ketones. 4462-4474 - Genki Kudo, Takumi Hirao, Ryunosuke Yoshino, Yasuteru Shigeta, Takatsugu Hirokawa:
Site Identification and Next Choice Protocol for Hit-to-Lead Optimization. 4475-4484 - Christian Kersten, Philippe Archambault, Luca P. Köhler:
Assessment of Nucleobase Protomeric and Tautomeric States in Nucleic Acid Structures for Interaction Analysis and Structure-Based Ligand Design. 4485-4499 - Fengjuan Huang, Jiahui Huang, Jiajia Yan, Yuying Liu, Jiangfang Lian, Qinxue Sun, Feng Ding, Yunxiang Sun:
Molecular Insights into the Effects of F16L and F19L Substitutions on the Conformation and Aggregation Dynamics of Human Calcitonin. 4500-4510 - Hyeonjun Kim, Youngshang Pak:
Isomerization Pathways of a Mismatched Base Pair of A:8OG in Free Duplex DNA. 4511-4517 - Hyeona Kang, Sun-Gu Lee:
Scalable Analysis of Dipole Moment Fluctuations for Characterizing Intermolecular Interactions and Structural Stability. 4518-4529 - Qian-Qian Wang, Jinshuai Song, Donghui Wei:
Origin of Chemoselectivity of Halohydrin Dehalogenase-Catalyzed Epoxide Ring-Opening Reactions. 4530-4541 - Nikolai V. Krivoshchapov, Michael G. Medvedev:
Accurate and Efficient Conformer Sampling of Cyclic Drug-Like Molecules with Inverse Kinematics. 4542-4552 - Christopher Vorreiter, Dina Robaa, Wolfgang Sippl:
Exploring Aromatic Cage Flexibility Using Cosolvent Molecular Dynamics Simulations─An In-Silico Case Study of Tudor Domains. 4553-4569 - Stefano Bosio, Mattia Bernetti, Walter Rocchia, Matteo Masetti:
Similarities and Differences in Ligand Binding to Protein and RNA Targets: The Case of Riboflavin. 4570-4586 - Lauri Urvas, Luca Chiesa, Guillaume Bret, Célien Jacquemard, Esther Kellenberger:
Benchmarking AlphaFold-Generated Structures of Chemokine-Chemokine Receptor Complexes. 4587-4600
Volume 64, Number 12, 2024
- Ethan Berger, Juha Niemelä, Outi Lampela, André H. Juffer, Hannu-Pekka Komsa:
Raman Spectra of Amino Acids and Peptides from Machine Learning Polarizabilities. 4601-4612 - Cailum M. K. Stienstra, Liam Hebert, Patrick Thomas, Alexander Haack, Jason Guo, W. Scott Hopkins:
Graphormer-IR: Graph Transformers Predict Experimental IR Spectra Using Highly Specialized Attention. 4613-4629 - Meitar Sela, Jonathan R. Church, Igor Schapiro, Dina Schneidman-Duhovny:
RhoMax: Computational Prediction of Rhodopsin Absorption Maxima Using Geometric Deep Learning. 4630-4639 - Maximilian G. Schuh, Davide Boldini, Stephan A. Sieber:
Synergizing Chemical Structures and Bioassay Descriptions for Enhanced Molecular Property Prediction in Drug Discovery. 4640-4650 - Roshni Bhatt, David Ryan Koes, Jacob D. Durrant:
CENsible: Interpretable Insights into Small-Molecule Binding with Context Explanation Networks. 4651-4660 - Patrick R. Fitzgerald, Anjali Dixit, Chris Zhang, David L. Mobley, Brian M. Paegel:
Building Block-Centric Approach to DNA-Encoded Library Design. 4661-4672 - Akie Kowaguchi, Paul E. Brumby, Kenji Yasuoka:
Hysteresis Elimination for an Anisotropic Liquid-Crystal Model via Molecule Design and Replica-Exchange Optimization. 4673-4686 - Francesco Rianjongdee, David Palmer, Stephen D. Pickett, Peter Pogány, Nicholas C. O. Tomkinson, Darren V. S. Green:
bbSelect - An Open-Source Tool for Performing a 3D Pharmacophore-Driven Diverse Selection of R-Groups. 4687-4699 - Tobias Rau, Michael Sedlmair, Andreas Köhn:
chARpack: The Chemistry Augmented Reality Package. 4700-4708 - Rutika Patel, Augustine Onyema, Phu K. Tang, Sharon M. Loverde:
Conformational Dynamics of the Nucleosomal Histone H2B Tails Revealed by Molecular Dynamics Simulations. 4709-4726 - Patrick Kunzmann, Jan Hendrik Krumbach, Andrea Saponaro, Anna Moroni, Gerhard Thiel, Kay Hamacher:
Anisotropic Network Analysis of Open/Closed HCN4 Channel Advocates Asymmetric Subunit Cooperativity in cAMP Modulation of Gating. 4727-4738 - Xinpei Wang, Xu Chen, Zhidong Chen, Wanting Xu, Ruizhi Lai, Xiaohui Qiu, Zekai Zeng, Chenglin Wang, Zhe Wang, Junqing Wang:
Integrated Anchored Stapling and Hierarchical Dynamics: MSICDA-Driven CREBBP Bromodomain Inhibition. 4739-4758 - Felipe Bravo-Moraga, Mauricio Bedoya, Ariela Vergara Jaque, Jans H. Alzate-Morales:
Understanding the Differences of Danusertib's Residence Time in Aurora Kinases A/B: Dissociation Paths and Key Residues Identified using Conventional and Enhanced Molecular Dynamics Simulations. 4759-4772 - Kecheng Yang, Hongmin Liu:
Mining the Dynamical Properties of Substrate and FAD Binding Pockets of LSD1: Hints for New Inhibitor Design Direction. 4773-4780 - Maria Pechlaner, Wilfred F. van Gunsteren, Lorna J. Smith, Bartosz Stankiewicz, Lukas N. Wirz, Niels Hansen:
Molecular Structure Refinement Based on Residual Dipolar Couplings: A Comparison of the Molecular Rotational-Sampling Method with the Alignment-Tensor Approach. 4781-4801 - Jesús Lucia-Tamudo, Sergio Díaz-Tendero, Juan J. Nogueira:
Modeling One-Electron Oxidation Potentials and Hole Delocalization in Double-Stranded DNA by Multilayer and Dynamic Approaches. 4802-4810 - Dongxiao Hao, Li-na Niu:
Computational Study on the Wealth Conformations of Hepatitis C Virus Envelope Glycoprotein 2 and Role of Its Glycan Coat. 4811-4821 - Muyun Lihan, Emad Tajkhorshid:
Improved Highly Mobile Membrane Mimetic Model for Investigating Protein-Cholesterol Interactions. 4822-4834 - Hao Guo, Zheyuan Shen, Yong-yi Yuan, Rou-fen Chen, Jing-yi Yang, Xing-chen Liu, Qing Zhang, Qian-ying Pan, Jian-jun Ding, Xin-jun He, Qing-nan Zhang, Xiaowu Dong, Ke-shu Zhou:
Discovery of a Novel and Potent LCK Inhibitor for Leukemia Treatment via Deep Learning and Molecular Docking. 4835-4849 - Martina Piga, Zoltán Varga, Adam Feher, Ferenc Papp, Eva Korpos, Kavya C. Bangera, Rok Frlan, Janez Ilas, Jaka Dernovsek, Tihomir Tomasic, Nace Zidar:
Identification of a Novel Structural Class of HV1 Inhibitors by Structure-Based Virtual Screening. 4850-4862 - Qin Zeng, Guangpeng Meng, Bingyu Zhao, Haodian Lin, Yuqing Guan, Xiaobin Qin, Yu Yuan, Yuanbo Li, Qiantao Wang:
Peptide Drug Design Using Alchemical Free Energy Calculation: An Application and Validation on Agonists of Ghrelin Receptor. 4863-4876 - Luosen Wang, Jie Hou, Peng Cao, Zhiying Yao, Shijun Wang, Yuying Zhang, Sheng Wang, Haoliang Yuan, Liu Liu:
Design, Synthesis, and Biological Evaluation of Chroman Derivatives as PD-1/PD-L1 Antagonists. 4877-4896 - Sita Sirisha Madugula, Pranav Pujar, Bharani Nammi, Shouyi Wang, Vindi M. Jayasinghe-Arachchige, Tyler Pham, Dominic Mashburn, Maria Artiles, Jin Liu:
Identification of Family-Specific Features in Cas9 and Cas12 Proteins: A Machine Learning Approach Using Complete Protein Feature Spectrum. 4897-4911 - Marco Giulini, Raffaele Fiorentini, Luca Tubiana, Raffaello Potestio, Roberto Menichetti:
EXCOGITO, an Extensible Coarse-Graining Toolbox for the Investigation of Biomolecules by Means of Low-Resolution Representations. 4912-4927 - Xiang Du, Xinliang Sun, Min Li:
Knowledge Graph Convolutional Network with Heuristic Search for Drug Repositioning. 4928-4937
Volume 64, Number 13, 2024
- Kenneth M. Merz Jr., Guo-Wei Wei, Feng Zhu:
Editorial: Cutting-Edge Methodologies in Omics Data Analysis. 4939-4940 - Sadik Bhattarai, Hilal Tayara, Kil To Chong:
Advancing Peptide-Based Cancer Therapy with AI: In-Depth Analysis of State-of-the-Art AI Models. 4941-4957 - Xuefeng Bai, Yabo Xie, Xin Zhang, Honggui Han, Jian-Rong Li:
Evaluation of Open-Source Large Language Models for Metal-Organic Frameworks Research. 4958-4965 - Yifei Yue, Saad Aldin Mohamed, Jianwen Jiang:
Classifying and Predicting the Thermal Expansion Properties of Metal-Organic Frameworks: A Data-Driven Approach. 4966-4979 - Amit Ranjan, Adam Bess, Chris Alvin, Supratik Mukhopadhyay:
MDF-DTA: A Multi-Dimensional Fusion Approach for Drug-Target Binding Affinity Prediction. 4980-4990 - Abdallah Abou Hajal, Richard A. Bryce, Boulbaba Ben Amor, Noor Atatreh, Mohammad A. Ghattas:
Boosting the Accuracy and Chemical Space Coverage of the Detection of Small Colloidal Aggregating Molecules Using the BAD Molecule Filter. 4991-5005 - Matthew Glace, Roudabeh S. Moazeni-Pourasil, Daniel W. Cook, Thomas D. Roper:
Iterative Regression of Corrective Baselines (IRCB): A New Model for Quantitative Spectroscopy. 5006-5015 - Nanqi Hong, Dejun Jiang, Zhe Wang, Huiyong Sun, Hao Luo, Lingjie Bao, Mingli Song, Yu Kang, Tingjun Hou:
TransfIGN: A Structure-Based Deep Learning Method for Modeling the Interaction between HLA-A*02:01 and Antigen Peptides. 5016-5027 - Jungwoo Kim, Woojae Chang, Hyunjun Ji, Insuk Joung:
Quantum-Informed Molecular Representation Learning Enhancing ADMET Property Prediction. 5028-5040 - Fatma Cankara, Simge Senyuz, Ahenk Zeynep Sayin, Attila Gürsoy, Ozlem Keskin:
DiPPI: A Curated Data Set for Drug-like Molecules in Protein-Protein Interfaces. 5041-5051 - Yating Lin, Jun Xu, Qiong Gu:
FerroLigandDB: A Ferroptosis Ligand Database of Structure-Activity Relations. 5052-5062 - David F. Hahn, Vytautas Gapsys, Bert L. de Groot, David L. Mobley, Gary Tresadern:
Current State of Open Source Force Fields in Protein-Ligand Binding Affinity Predictions. 5063-5076 - Aditya Kulkarni, Michael Bortz, Karl-Heinz Küfer, Maximilian Kohns, Hans Hasse:
Hierarchical Multicriteria Optimization of Molecular Models of Water. 5077-5089 - Muhammad Haseeb, Yang Seon Choi, Mahesh Chandra Patra, Uisuk Jeong, Wang Hee Lee, Naila Qayyum, Hongjoon Choi, Wook Kim, Sangdun Choi:
Discovery of Novel Small Molecule Dual Inhibitor Targeting Toll-Like Receptors 7 and 9. 5090-5107 - Josh Kemppainen, Jacob R. Gissinger, S. Gowtham, Gregory M. Odegard:
LUNAR: Automated Input Generation and Analysis for Reactive LAMMPS Simulations. 5108-5126 - Ana M. Muñoz, Víctor H. Orozco, Lina M. Hoyos, Luis F. Giraldo, Cesar A. Pérez:
Rational Design of Molecularly Imprinted Polymers for Curcuminoids Binding: Computational and Experimental Approaches for the Selection of Functional Monomers. 5127-5139 - Isidora Diakogiannaki, Michail Papadourakis, Vasileia Spyridaki, Zoe Cournia, Andreas Koutselos:
Computational Investigation of BMAA and Its Carbamate Adducts as Potential GluR2 Modulators. 5140-5150 - Zakaria L. Dahmani, Ana Ligia Scott, Catherine Vénien-Bryan, David Perahia, Mauricio G. S. Costa:
MDFF_NM: Improved Molecular Dynamics Flexible Fitting into Cryo-EM Density Maps with a Multireplica Normal Mode-Based Search. 5151-5160 - Xin Xia, Yiping Liu, Chunhou Zheng, Xingyi Zhang, Qingwen Wu, Xin Gao, Xiangxiang Zeng, Yansen Su:
Evolutionary Multiobjective Molecule Optimization in an Implicit Chemical Space. 5161-5174 - Romain Launay, Sophie-Carole Chobert, Sophie S. Abby, Fabien Pierrel, Isabelle André, Jérémy Esque:
Structural Reconstruction of E. coli Ubi Metabolon Using an AlphaFold2-Based Computational Framework. 5175-5193 - Leon Wehrhan, Bettina G. Keller:
Prebound State Discovered in the Unbinding Pathway of Fluorinated Variants of the Trypsin-BPTI Complex Using Random Acceleration Molecular Dynamics Simulations. 5194-5206 - Yuan-Ling Xia, Wen-Wen Du, Yong-Ping Li, Yan Tao, Zhi-Bi Zhang, Song-Ming Liu, Yun-Xin Fu, Ke-Qin Zhang, Shu-Qun Liu:
Computational Insights into SARS-CoV-2 Main Protease Mutations and Nirmatrelvir Efficacy: The Effects of P132H and P132H-A173V. 5207-5218 - Qianjun Xu, Maohua Yang, Jie Ji, Jingwei Weng, Wenning Wang, Xin Xu:
Impact of Nonnative Interactions on the Binding Kinetics of Intrinsically Disordered p53 with MDM2: Insights from All-Atom Simulation and Markov State Model Analysis. 5219-5231 - Christian Seitz, Surl-Hee Ahn, Haixin Wei, Matson Kyte, Gregory M. Cook, Kurt L. Krause, James Andrew McCammon:
Targeting Tuberculosis: Novel Scaffolds for Inhibiting Cytochrome bd Oxidase. 5232-5241 - Andres S. Arango, Hyun Park, Emad Tajkhorshid:
Topological Learning Approach to Characterizing Biological Membranes. 5242-5252 - Pu Jiang, Cong Zhang, Hongshuang Wang, Penghui Li, Xiubo Du, Yibo Wang, Ekaterina Lyukmanova, Cong Lin, Xiaohui Wang:
Nicotine Enantioselectively Targets Myeloid Differentiation Protein 2 and Inhibits the Toll-like Receptor 4 Signaling. 5253-5261 - Bryan M. Delfing, Xavier E. Laracuente, William Jeffries, Xingyu Luo, Audrey Olson, Kenneth W. Foreman, Greg Petruncio, Kyung Hyeon Lee, Mikell Paige, Kylene Kehn-Hall, Christopher Lockhart, Dmitri K. Klimov:
Competitive Binding of Viral Nuclear Localization Signal Peptide and Inhibitor Ligands to Importin-α Nuclear Transport Protein. 5262-5272 - Jingwei Gao, Cong Zhang, Hangyu Xu, Tianshu Zhang, Hongshuang Wang, Yibo Wang, Xiaohui Wang:
Dissecting the Role of the Hydroxyl Moiety at C14 in (+)-Opioid-Based TLR4 Antagonists via Wet-Lab Experiments and Molecular Dynamics Simulations. 5273-5284 - David Ricardo Figueroa Blanco, Pietro Vidossich, Marco de Vivo:
Correct Nucleotide Selection Is Confined at the Binding Site of Polymerase Enzymes. 5285-5294 - Magnus Lundborg, Christian Wennberg, Erik Lindahl, Lars Norlén:
Simulating the Skin Permeation Process of Ionizable Molecules. 5295-5302 - Xinjie Fan, Xiaohan Zhang, Jiajia Yan, Huan Xu, Wenhui Zhao, Feng Ding, Fengjuan Huang, Yunxiang Sun:
Computational Investigation of Coaggregation and Cross-Seeding between Aβ and hIAPP Underpinning the Cross-Talk in Alzheimer's Disease and Type 2 Diabetes. 5303-5316 - Siqi Chen, Nan Gao, Chunzhi Li, Fei Zhai, Xiwei Jiang, Peng Zhang, Jibin Guan, Kefeng Li, Rongwu Xiang, Guixia Ling:
DrugSK: A Stacked Ensemble Learning Framework for Predicting Drug Combinations of Multiple Diseases. 5317-5327 - Kriti Shukla, Kelvin Idanwekhai, Martin Naradikian, Stephanie Ting, Stephen P. Schoenberger, Elizabeth Brunk:
Machine Learning of Three-Dimensional Protein Structures to Predict the Functional Impacts of Genome Variation. 5328-5343 - Merveille K. I. Eguida, Guillaume Bret, François Sindt, Fengling Li, Irene Chau, Suzanne Ackloo, Cheryl H. Arrowsmith, Albina Bolotokova, Pegah Ghiabi, Elisa Gibson, Levon Halabelian, Scott Houliston, Rachel J. Harding, Ashley Hutchinson, Peter Loppnau, Sumera Perveen, Almagul Seitova, Hong Zeng, Matthieu Schapira, Didier Rognan:
Subpocket Similarity-Based Hit Identification for Challenging Targets: Application to the WDR Domain of LRRK2. 5344-5355 - Petra Kührová, Vojtech Mlýnský, Michal Otyepka, Jirí Sponer, Pavel Banás:
Correction to "Sensitivity of the RNA Structure to Ion Conditions as Probed by Molecular Dynamics Simulations of Common Canonical RNA Duplexes". 5356
Volume 64, Number 14, 2024
- Benjamin Ries, Irfan Alibay, Nithishwer Mouroug Anand, Philip C. Biggin, Aniket Magarkar:
Automated Absolute Binding Free Energy Calculation Workflow for Drug Discovery. 5357-5364 - Lewis H. Mervin, Alexey Voronov, Mikhail Kabeshov, Ola Engkvist:
QSARtuna: An Automated QSAR Modeling Platform for Molecular Property Prediction in Drug Design. 5365-5374 - Inbal Tuvi-Arad, Yaffa Shalit, Gil Alon:
CSM Software: Continuous Symmetry and Chirality Measures for Quantitative Structural Analysis. 5375-5380 - Chao Shen, Jianfei Song, Chang-Yu Hsieh, Dong-Sheng Cao, Yu Kang, Wenling Ye, Zhenxing Wu, Jike Wang, Odin Zhang, Xujun Zhang, Hao Zeng, Heng Cai, Yu Chen, Linkang Chen, Hao Luo, Xinda Zhao, Tianye Jian, Tong Chen, Dejun Jiang, Mingyang Wang, Qing Ye, Jialu Wu, Hongyan Du, Hui Shi, Yafeng Deng, Tingjun Hou:
DrugFlow: An AI-Driven One-Stop Platform for Innovative Drug Discovery. 5381-5391 - Letizia Fiorucci, Marco Schiavina, Isabella C. Felli, Roberta Pierattelli, Enrico Ravera:
Are Protein Conformational Ensembles in Agreement with Experimental Data? A Geometrical Interpretation of the Problem. 5392-5401 - Stefan Semrau:
Neural Network-Based Filter Design for Compressive Raman Classification of Cells. 5402-5412 - Haihan Liu, Baichun Hu, Peiying Chen, Xiao Wang, Hanxun Wang, Shizun Wang, Jian Wang, Bin Lin, Mao-Sheng Cheng:
Docking Score ML: Target-Specific Machine Learning Models Improving Docking-Based Virtual Screening in 155 Targets. 5413-5426 - Chengtao Pu, Lingxi Gu, Yuxuan Hu, Weijie Han, Xiaohe Xu, Haichun Liu, Yadong Chen, Yanmin Zhang:
Prediction of Human Liver Microsome Clearance with Chirality-Focused Graph Neural Networks. 5427-5438 - Zachary J. Gale-Day, Laura Shub, Kangway V. Chuang, Michael J. Keiser:
Proximity Graph Networks: Predicting Ligand Affinity with Message Passing Neural Networks. 5439-5450 - Gökhan Tahil, Fabien Delorme, Daniel Le Berre, Éric Monflier, Adlane Sayede, Sébastien Tilloy:
Stereoisomers Are Not Machine Learning's Best Friends. 5451-5469 - Junren Li, Kangjie Lin, Jianfeng Pei, Luhua Lai:
Challenging Complexity with Simplicity: Rethinking the Role of Single-Step Models in Computer-Aided Synthesis Planning. 5470-5479 - Hongle An, Xuyang Liu, Wensheng Cai, Xueguang Shao:
AttenGpKa: A Universal Predictor of Solvation Acidity Using Graph Neural Network and Molecular Topology. 5480-5491 - Peter Eckmann, Jake Anderson, Rose Yu, Michael K. Gilson:
Ligand-Based Compound Activity Prediction via Few-Shot Learning. 5492-5499 - Shuyu Wang, Hongxing Yue, Xiaoming Yuan:
Accelerating Polymer Discovery with Uncertainty-Guided PGCNN: Explainable AI for Predicting Properties and Mechanistic Insights. 5500-5509 - Manuel Carrer, Henrique M. Cezar, Sigbjørn Løland Bore, Morten Ledum, Michele Cascella:
Learning Force Field Parameters from Differentiable Particle-Field Molecular Dynamics. 5510-5520 - Vincent Fan, Yujie Qian, Alex Wang, Amber Wang, Connor W. Coley, Regina Barzilay:
OpenChemIE: An Information Extraction Toolkit for Chemistry Literature. 5521-5534 - Fangting Li, Kun Lv, Xiaohua Liu, Yuqiao Zhou, Kai Liu:
Accurately Computing the Interacted Volume of Molecules over Their 3D Mesh Models. 5535-5546 - Linh Ho Manh, Victoria C. P. Chen, Jay M. Rosenberger, Shouyi Wang, Yujing Yang, Kevin A. Schug:
Prediction of Vacuum Ultraviolet/Ultraviolet Gas-Phase Absorption Spectra Using Molecular Feature Representations and Machine Learning. 5547-5556 - Itsuki Maeda, Shunsuke Tamura, Yoshihiro Ogura, Takayuki Serizawa, Takashi Shimada, Ryo Kunimoto, Tomoyuki Miyao:
Scaffold-Hopped Compound Identification by Ligand-Based Approaches with a Prospective Affinity Test. 5557-5569 - Ciceron Ayala-Orzoco, Hamid Teimouri, Angela Medvedeva, Bowen Li, Alex Lathem, Gang Li, Anatoly B. Kolomeisky, James M. Tour:
Chemoinformatics Insights on Molecular Jackhammers and Cancer Cells. 5570-5579 - Ranabir Majumder, Shreya Banerjee, Sayan Paul, Saugat Mondal, Madhurima Mandal, Priya Ghosh, Debjit Maity, Anakuthil Anoop, N. D. Pradeep Singh, Mahitosh Mandal:
Riboflavin-Induced DNA Damage and Anticancer Activity in Breast Cancer Cells under Visible Light: A TD-DFT and In Vitro Study. 5580-5589 - Debashree Chakraborty, Omkar Singh, Divya Parameswaran:
Study of Correlated Motions to Detect the Conformational Transitions of the Intrinsically Disordered Sheep Prion Peptide. 5590-5603 - Vicente Martí-Centelles, Tomasz K. Piskorz, Fernanda Duarte:
CageCavityCalc (C3): A Computational Tool for Calculating and Visualizing Cavities in Molecular Cages. 5604-5616 - Tao Liu, Lena Simine:
DeltaGzip: Computing Biopolymer-Ligand Binding Affinity via Kolmogorov Complexity and Lossless Compression. 5617-5623 - Zijing Tian, Yan Dai, Feng Hu, Zihao Shen, Hongling Xu, Hongwen Zhang, Jinhang Xu, Yuting Hu, Yanyan Diao, Honglin Li:
Enhancing Chemical Reaction Monitoring with a Deep Learning Model for NMR Spectra Image Matching to Target Compounds. 5624-5633 - Emanuele Falbo, Antonio Lavecchia:
HessFit: A Toolkit to Derive Automated Force Fields from Quantum Mechanical Information. 5634-5645 - Shuo Liu, Jialiang Yu, Ningxi Ni, Zidong Wang, Mengyun Chen, Yuquan Li, Chen Xu, Yahao Ding, Jun Zhang, Xiaojun Yao, Huanxiang Liu:
Versatile Framework for Drug-Target Interaction Prediction by Considering Domain-Specific Features. 5646-5656 - Monica P. Barron, Jonah Z. Vilseck:
A λ-Dynamics Investigation of Insulin Wakayama and Other A3 Variant Binding Affinities to the Insulin Receptor. 5657-5670 - Han Zhang, Wonpil Im:
Ligand Binding Affinity Prediction for Membrane Proteins with Alchemical Free Energy Calculation Methods. 5671-5679 - Zhiyu Zhao, Emad Tajkhorshid:
GOLEM: Automated and Robust Cryo-EM-Guided Ligand Docking with Explicit Water Molecules. 5680-5690 - Jakob Liu, Andreas Fischer, Monika Cserjan-Puschmann, Nico Lingg, Chris Oostenbrink:
Caspase-Based Fusion Protein Technology: Substrate Cleavability Described by Computational Modeling and Simulation. 5691-5700 - Lisa Lombardo, Salvatore Mirabile, Rosaria Gitto, Giuseppe Cosentino, Stefano Alcaro, Maria Dichiara, Agostino Marrazzo, Emanuele Amata, Francesco Ortuso, Laura De Luca:
Exploring Structural Requirements for Sigma-1 Receptor Linear Ligands: Experimental and Computational Approaches. 5701-5711 - Nanako Inoue, Tomokazu Shibata, Yusuke Tanaka, Hiromu Taguchi, Ryusuke Sawada, Kenshin Goto, Shogo Momokita, Morihiro Aoyagi, Takashi Hirao, Yoshihiro Yamanishi:
Revealing Comprehensive Food Functionalities and Mechanisms of Action through Machine Learning. 5712-5724 - Lantian Yao, Peilin Xie, Jiahui Guan, Chia-Ru Chung, Yixian Huang, Yuxuan Pang, Huacong Wu, Ying-Chih Chiang, Tzong-Yi Lee:
CapsEnhancer: An Effective Computational Framework for Identifying Enhancers Based on Chaos Game Representation and Capsule Network. 5725-5736
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