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ORCIDJournal of Chemical Information and Modeling, Volume 63
Volume 63, Number 1, January 2023
- Issue Publication Information.
- Issue Editorial Masthead.
- Kenneth M. Merz Jr., Guo-Wei Wei, Feng Zhu
:
Editorial: Machine Learning in Bio-cheminformatics. 1 - Martin Stroet, Stephen Sanderson, Audrey V. Sanzogni, Sharif Nada, Thomas Lee, Bertrand Caron, Alan E. Mark, Paul L. Burn:
PyThinFilm: Automated Molecular Dynamics Simulation Protocols for the Generation of Thin Film Morphologies. 2-8 - Ahmet Yildirim, Mustafa Tekpinar:
Building Quantitative Bridges between Dynamics and Sequences of SARS-CoV-2 Main Protease and a Diverse Set of Thirty-Two Proteins. 9-19 - Rui P. P. Neves, Maria João Ramos, Pedro Alexandrino Fernandes:
Engineering DszC Mutants from Transition State Macrodipole Considerations and Evolutionary Sequence Analysis. 20-26 - Daniel Vella, Jean-Paul Ebejer:
Few-Shot Learning for Low-Data Drug Discovery. 27-42 - Weimin Zhu, Yi Zhang, Duancheng Zhao, Jianrong Xu, Ling Wang:
HiGNN: A Hierarchical Informative Graph Neural Network for Molecular Property Prediction Equipped with Feature-Wise Attention. 43-55 - Maria Vittoria Togo, Fabrizio Mastrolorito, Fulvio Ciriaco, Daniela Trisciuzzi, Anna Rita Tondo, Nicola Gambacorta, Loredana Bellantuono, Alfonso Monaco, Francesco Leonetti, Roberto Bellotti, Cosimo Damiano Altomare, Nicola Amoroso, Orazio Nicolotti:
TIRESIA: An eXplainable Artificial Intelligence Platform for Predicting Developmental Toxicity. 56-66 - Hao Tian, Xi Jiang, Sian Xiao, Hunter La Force, Eric C. Larson, Peng Tao:
LAST: Latent Space-Assisted Adaptive Sampling for Protein Trajectories. 67-75 - Ryo Kawada, Katsuhiro Endo, Kenji Yasuoka, Hidekazu Kojima, Nobuyuki Matubayasi:
Prediction of Water Diffusion in Wide Varieties of Polymers with All-Atom Molecular Dynamics Simulations and Deep Generative Models. 76-86 - Omer Kaspi, Osnat Israelsohn-Azulay, Zidon Yigal, Hila Rosengarten, Matea Krmpotic, Sabrina Gouasmia, Iva Bogdanovic-Radovic, Pasi Jalkanen, Anna Liski, Kenichiro Mizohata, Jyrki Räisänen, Zsolt Kasztovszky, Ildikó Harsányi, Raghunath Acharya, Pradeep K. Pujari, Molnár Mihály, Mihaly Braun, Nahum Shabi, Olga Girshevitz, Hanoch Senderowitz:
Toward Developing Techniques─Agnostic Machine Learning Classification Models for Forensically Relevant Glass Fragments. 87-100 - Jörg Heider, Jonas Kilian, Aleksandra Garifulina, Steffen Hering, Thierry Langer, Thomas Seidel:
Apo2ph4: A Versatile Workflow for the Generation of Receptor-based Pharmacophore Models for Virtual Screening. 101-110 - Teng-Zhi Long, Shao-Hua Shi, Shao Liu, Ai-Ping Lu, Zhao-Qian Liu, Min Li, Tingjun Hou, Dong-Sheng Cao:
Structural Analysis and Prediction of Hematotoxicity Using Deep Learning Approaches. 111-125 - Omri Wolk, Amiram Goldblum:
Predicting the Likelihood of Molecules to Act as Modulators of Protein-Protein Interactions. 126-137 - Daniel Sethio, Poongavanam Vasanthanathan, Ruisheng Xiong, Mohit Tyagi, Duc Duy Vo, Roland Lindh, Jan Kihlberg:
Simulation Reveals the Chameleonic Behavior of Macrocycles. 138-146 - Paul L. Türtscher, Markus Reiher:
Pathfinder─Navigating and Analyzing Chemical Reaction Networks with an Efficient Graph-Based Approach. 147-160 - Mirko Paulikat, Daniele Vitone, Florian Karl Schackert, Nils Schuth, Alessandra Barbanente, GiovanniMaria Piccini, Emiliano Ippoliti, Giulia Rossetti, Adam H. Clark, Maarten Nachtegaal, Michael Haumann, Holger Dau, Paolo Carloni, Silvano Geremia, Rita De Zorzi, Liliana Quintanar, Fabio Arnesano:
Molecular Dynamics and Structural Studies of Zinc Chloroquine Complexes. 161-172 - Chen Qian, Xin Zhou, Jessica Rehmel, James P. Steele, Kjell A. Svensson, James P. Beck, Erik J. Hembre, Junliang Hao:
Ensemble Docking Approach to Mitigate Pregnane X Receptor-Mediated CYP3A4 Induction Risk. 173-186 - Andrey I. Frolov, Sunay V. Chankeshwara, Zeyed Abdulkarim, Gian Marco Ghiandoni:
pIChemiSt ─ Free Tool for the Calculation of Isoelectric Points of Modified Peptides. 187-196 - Oriol Gracia Carmona, Chris Oostenbrink:
Accelerated Enveloping Distribution Sampling (AEDS) Allows for Efficient Sampling of Orthogonal Degrees of Freedom. 197-207 - Chythra J. N., Sairam S. Mallajosyula:
Impact of Polarization on the Ring Puckering Dynamics of Hexose Monosaccharides. 208-223 - Nibedita Ray Chaudhuri, Shubhra Ghosh Dastidar:
Allosteric Boost by TAB1 on the TAK1 Kinase Favorably Sculpts the Thermodynamic Landscape of Activation. 224-239 - Kei Moritsugu, Toru Ekimoto, Mitsunori Ikeguchi, Akinori Kidera:
Binding and Unbinding Pathways of Peptide Substrates on the SARS-CoV-2 3CL Protease. 240-250 - Francesco Pettini, Carmen Domene, Simone Furini:
Early Steps in C-Type Inactivation of the hERG Potassium Channel. 251-258 - Ryuhei Harada, Rikuri Morita, Yasuteru Shigeta:
Free-Energy Profiles for Membrane Permeation of Compounds Calculated Using Rare-Event Sampling Methods. 259-269 - Leslie Sánchez, Fabiola E. Medina, Fernanda Mendoza, Camilo Febres-Molina, Gonzalo A. Jaña:
Elucidation of the Reaction Mechanism of Cavia porcellus l-Asparaginase: A QM/MM Study. 270-280 - Till El Harrar, Holger Gohlke:
Cumulative Millisecond-Long Sampling for a Comprehensive Energetic Evaluation of Aqueous Ionic Liquid Effects on Amino Acid Interactions. 281-298 - Anastasiia Delova, Raúl Losantos, Jérémy Pecourneau, Yann Bernhard, Maxime Mourer, Andreea Pasc, Antonio Monari:
Perturbation of Lipid Bilayers by Biomimetic Photoswitches Based on Cyclocurcumin. 299-307 - Yuying Liu, Ying Wang, Yu Zhang, Yu Zou, Guanghong Wei, Feng Ding, Yunxiang Sun:
Structural Perturbation of Monomers Determines the Amyloid Aggregation Propensity of Calcitonin Variants. 308-320 - Aristarc Suriñach, Adam Hospital, Yvonne Westermaier, Luis Jordà, Sergi Orozco-Ruiz, Daniel Beltrán, Francesco Colizzi, Pau Andrio, Robert Soliva, Martí Municoy, Josep Lluis Gelpí, Modesto Orozco:
High-Throughput Prediction of the Impact of Genetic Variability on Drug Sensitivity and Resistance Patterns for Clinically Relevant Epidermal Growth Factor Receptor Mutations from Atomistic Simulations. 321-334 - Jiahui Chen, Rui Wang, Yuta Hozumi, Gengzhuo Liu, Yuchi Qiu, Xiaoqi Wei, Guo-Wei Wei:
Emerging Dominant SARS-CoV-2 Variants. 335-342 - Luca Torielli, Stefano A. Serapian, Lara Mussolin, Elisabetta Moroni, Giorgio Colombo:
Integrating Protein Interaction Surface Prediction with a Fragment-Based Drug Design: Automatic Design of New Leads with Fragments on Energy Surfaces. 343-353 - Madelyn Smith, Pengfei Li:
Molecular Insights into the Calcium Binding in Troponin C through a Molecular Dynamics Study. 354-361 - Xiaoyue Ji, Hao Liu, Yangpeng Zhang, Jun Chen, Hai-Feng Chen:
Personal Precise Force Field for Intrinsically Disordered and Ordered Proteins Based on Deep Learning. 362-374 - Reem A. Alkhodier, Sushil Kumar Mishra, Robert J. Doerksen, David A. Colby:
Comparison of Conformational Analyses of Naturally Occurring Flavonoid-O-Glycosides with Unnatural Flavonoid-CF2-Glycosides Using Molecular Modeling. 375-386 - Marley L. Samways, Hannah E. Bruce Macdonald, Richard D. Taylor, Jonathan W. Essex:
Water Networks in Complexes between Proteins and FDA-Approved Drugs. 387-396 - Yan Liu, He Yan, Long-Chen Shen, Dong-Jun Yu:
Learning Cell Annotation under Multiple Reference Datasets by Multisource Domain Adaptation. 397-405 - Stefano Costanzi, Charlotte K. Slavick, Brent O. Hutcheson, Gregory D. Koblentz, Richard T. Cupitt:
Correction to "Lists of Chemical Warfare Agents and Precursors from International Nonproliferation Frameworks: Structural Annotation and Chemical Fingerprint Analysis". 406
Volume 63, Number 2, January 2023
- Diego Enry Barreto Gomes, Katia Galentino, Marion Sisquellas, Luca Monari, Cédric Bouysset, Marco Cecchini:
ChemFlow─From 2D Chemical Libraries to Protein-Ligand Binding Free Energies. 407-411 - Kristian Kríz, Lisa Schmidt, Alfred T. Andersson, Marie-Madeleine Walz, David van der Spoel:
An Imbalance in the Force: The Need for Standardized Benchmarks for Molecular Simulation. 412-431 - Raghad Al-Jarf, Simon Tang, Douglas E. V. Pires, David B. Ascher:
embryoTox: Using Graph-Based Signatures to Predict the Teratogenicity of Small Molecules. 432-441 - Raya Stoyanova, Paul Maximilian Katzberger, Leonid Komissarov, Aous Khadhraoui, Lisa Sach-Peltason, Katrin Groebke Zbinden, Torsten Schindler, Nenad Manevski:
Computational Predictions of Nonclinical Pharmacokinetics at the Drug Design Stage. 442-458 - Cesare Roncaglia, Riccardo Ferrando:
Machine Learning Assisted Clustering of Nanoparticle Structures. 459-473 - Iori Azuma, Tadahaya Mizuno, Hiroyuki Kusuhara:
NRBdMF: A Recommendation Algorithm for Predicting Drug Effects Considering Directionality. 474-483 - Ye Buehler, Jean-Louis Reymond:
Molecular Framework Analysis of the Generated Database GDB-13s. 484-492 - Yangcheng Ai, Zichao Yang, Zilong Yang, Shanhe Wan, Chunhui Huang, Chuan Huang, Mingxia Li, Zhonghuang Li, Jiajie Zhang, Tingting Zhang:
Discovery and Computational Studies of Potent Covalent Kinase Inhibitors with α-Substituent Electrophiles Targeting Cysteine. 493-506 - Sebastián Adolfo Cuesta, Martín Moreno, Romina A. López, José Ramón Mora, José Luis Paz, Edgar Márquez:
ElectroPredictor: An Application to Predict Mayr's Electrophilicity E through Implementation of an Ensemble Model Based on Machine Learning Algorithms. 507-521 - Reecan J. Juarez, Yaoyukun Jiang, Matthew Tremblay, Qianzhen Shao, A. James Link, Zhongyue J. Yang:
LassoHTP: A High-Throughput Computational Tool for Lasso Peptide Structure Construction and Modeling. 522-530 - Luca Mollica, Gabriele Giachin:
Recognition Mechanisms between a Nanobody and Disordered Epitopes of the Human Prion Protein: An Integrative Molecular Dynamics Study. 531-545 - Alexander Zlobin, Julia Belyaeva, Andrey Golovin:
Challenges in Protein QM/MM Simulations with Intra-Backbone Link Atoms. 546-560 - Yishui Li, Runduo Liu, Jie Liu, Haibin Luo, Chengkun Wu, Zhe Li:
An Open Source Graph-Based Weighted Cycle Closure Method for Relative Binding Free Energy Calculations. 561-570 - Namita Dube, Sabab Hasan Khan, Riley Sasse, C. Denise Okafor:
Identification of an Evolutionarily Conserved Allosteric Network in Steroid Receptors. 571-582 - Filipp Gusev, Evgeny Gutkin, Maria Kurnikova, Olexandr Isayev:
Active Learning Guided Drug Design Lead Optimization Based on Relative Binding Free Energy Modeling. 583-594 - Federico N. Pedron, Andresa Messias, Ari Zeida, Adrian E. Roitberg, Dario A. Estrin:
Novel Lennard-Jones Parameters for Cysteine and Selenocysteine in the AMBER Force Field. 595-604 - Xiaokun Hong, Kaiyuan Song, Mueed Ur Rahman, Ting Wei, Yan Zhang, Lin-Tai Da, Hai-Feng Chen:
Phosphorylation Regulation Mechanism of β2 Integrin for the Binding of Filamin Revealed by Markov State Model. 605-618 - Jie Gao, Yaoliang Zhang, Lin Yu, Yuejuan Li, Shumin Liao, Jian Wang, Lijie Guan:
Identification of Enolase 1 as a Potential Target for Magnaporthe oryzae: Integrated Proteomic and Molecular Dynamics Simulation. 619-632 - Natasha Gupta Vergara, Megan Gatchel, Cameron F. Abrams:
Entropic Overcompensation of the N501Y Mutation on SARS-CoV-2 S Binding to ACE2. 633-642 - Ke Zuo, Riccardo Capelli, Giulia Rossetti, Rachel Nechushtai, Paolo Carloni:
Predictions of the Poses and Affinity of a Ligand over the Entire Surface of a NEET Protein: The Case of Human MitoNEET. 643-654 - Zakir Ali, Ambika Goyal, Ayush Jhunjhunwala, Abhijit Mitra, John F. Trant, Purshotam Sharma:
Structural and Energetic Features of Base-Base Stacking Contacts in RNA. 655-669 - Rojalin Pradhan, Sibarama Panigrahi, Prabhat K. Sahu:
Conformational Search for the Building Block of Proteins Based on the Gradient Gravitational Search Algorithm (ConfGGS) Using Force Fields: CHARMM, AMBER, and OPLS-AA. 670-690
Volume 63, Number 3, February 2023
- Fabio Urbina, Filippa Lentzos, Cédric Invernizzi, Sean Ekins:
Preventing AI From Creating Biochemical Threats. 691-694 - Yan A. Ivanenkov, Daniil Polykovskiy, Dmitry Bezrukov, Bogdan Zagribelnyy, Vladimir Aladinskiy, Petrina Kamya, Alex Aliper, Feng Ren, Alex Zhavoronkov:
Chemistry42: An AI-Driven Platform for Molecular Design and Optimization. 695-701 - Cécile Hilpert, Louis Beranger, Paulo Cesar Telles de Souza, Petteri A. Vainikka, Vincent Nieto, Siewert J. Marrink, Luca Monticelli, Guillaume Launay:
Facilitating CG Simulations with MAD: The MArtini Database Server. 702-710 - Madushanka Manathunga, Hasan Metin Aktulga, Andreas W. Götz, Kenneth M. Merz Jr.:
Quantum Mechanics/Molecular Mechanics Simulations on NVIDIA and AMD Graphics Processing Units. 711-717 - Mateusz K. Bieniek, Alexander D. Wade, Agastya P. Bhati, Shunzhou Wan, Peter V. Coveney:
TIES 2.0: A Dual-Topology Open Source Relative Binding Free Energy Builder with Web Portal. 718-724 - Adem R. N. Aouichaoui, Fan Fan, Seyed Soheil Mansouri, Jens Abildskov, Gürkan Sin:
Combining Group-Contribution Concept and Graph Neural Networks Toward Interpretable Molecular Property Models. 725-744 - Lincan Fang, Xiaomi Guo, Milica Todorovic, Patrick Rinke, Xi Chen:
Exploring the Conformers of an Organic Molecule on a Metal Cluster with Bayesian Optimization. 745-752 - Frank W. Marrs, Jack V. Davis, Alexandra C. Burch, Geoffrey W. Brown, Nicholas Lease, Patricia L. Huestis, Marc J. Cawkwell, Virginia W. Manner:
Chemical Descriptors for a Large-Scale Study on Drop-Weight Impact Sensitivity of High Explosives. 753-769 - Yixiang Ruan, Sen Lin, Yiming Mo:
AROPS: A Framework of Automated Reaction Optimization with Parallelized Scheduling. 770-781 - Donghan Wang, Wenze Li, Xu Dong, Hongzhi Li, Lihong Hu:
TFRegNCI: Interpretable Noncovalent Interaction Correction Multimodal Based on Transformer Encoder Fusion. 782-793 - Kohei Nemoto, Hiromasa Kaneko:
De Novo Direct Inverse QSPR/QSAR: Chemical Variational Autoencoder and Gaussian Mixture Regression Models. 794-805 - Yufeng Liu, Zhenyu Li:
Predict Ionization Energy of Molecules Using Conventional and Graph-Based Machine Learning Models. 806-814 - Yuqing Yang, Dongping Liu, Zhendong Hua, Peng Xu, Youmei Wang, Bin Di, Jun Liao, Mengxiang Su:
Machine Learning-Assisted Rapid Screening of Four Types of New Psychoactive Substances in Drug Seizures. 815-825 - Adnan Khan, Jamal Uddin, Farman Ali, Harish Kumar, Wajdi Alghamdi, Aftab Ahmad:
AFP-SPTS: An Accurate Prediction of Antifreeze Proteins Using Sequential and Pseudo-Tri-Slicing Evolutionary Features with an Extremely Randomized Tree. 826-834 - Haiping Zhang, Konda Mani Saravanan, Yanjie Wei, Yang Jiao, Yang Yang, Yi Pan, Xuli Wu, John Z. H. Zhang:
Deep Learning-Based Bioactive Therapeutic Peptide Generation and Screening. 835-845 - Tuan Xu, Md Kabir, Srilatha Sakamuru, Pranav Shah, Elias C. Padilha, Deborah K. Ngan, Menghang Xia, Xin Xu, Anton Simeonov, Ruili Huang:
Predictive Models for Human Cytochrome P450 3A7 Selective Inhibitors and Substrates. 846-855 - Seungchan An, Seok Young Hwang, Junpyo Gong, Sungjin Ahn, In Guk Park, Soyeon Oh, Young-Won Chin, Minsoo Noh:
Computational Prediction of the Phenotypic Effect of Flavonoids on Adiponectin Biosynthesis. 856-869 - Sneha Thomas, Kevin S. Silmore, Piyush Sharma, Ananth Govind Rajan:
Enumerating Stable Nanopores in Graphene and Their Geometrical Properties Using the Combinatorics of Hexagonal Lattices. 870-881 - Álvaro Pérez-Barcia, Gustavo Cárdenas, Juan J. Nogueira, Marcos Mandado:
Effect of the QM Size, Basis Set, and Polarization on QM/MM Interaction Energy Decomposition Analysis. 882-897 - Francesca Peccati, Sara Alunno-Rufini, Gonzalo Jiménez-Osés:
Accurate Prediction of Enzyme Thermostabilization with Rosetta Using AlphaFold Ensembles. 898-909 - Abhishek Acharya, Ishan Ghai, Claudio Piselli, Jigneshkumar Dahyabhai Prajapati, Roland Benz, Mathias Winterhalter, Ulrich Kleinekathöfer:
Conformational Dynamics of Loop L3 in OmpF: Implications toward Antibiotic Translocation and Voltage Gating. 910-927 - Efpraxia Tzortzini, Robin A. Corey, Antonios Kolocouris:
Comparative Study of Receptor-, Receptor State-, and Membrane-Dependent Cholesterol Binding Sites in A2A and A1 Adenosine Receptors Using Coarse-Grained Molecular Dynamics Simulations. 928-949 - Santiago Movilla, Sergio Martí, Maite Roca, Vicent Moliner:
Computational Study of the Inhibition of RgpB Gingipain, a Promising Target for the Treatment of Alzheimer's Disease. 950-958 - Krishna Prasad Ghanta, Souvik Mondal, Timir Hajari, Sanjoy Bandyopadhyay:
Impact of an Ionic Liquid on Amino Acid Side Chains: A Perspective from Molecular Simulation Studies. 959-972 - Patrice Koehl, Arseniy V. Akopyan, Herbert Edelsbrunner:
Computing the Volume, Surface Area, Mean, and Gaussian Curvatures of Molecules and Their Derivatives. 973-985 - Yazdan Maghsoud, Erik Antonio Vázquez-Montelongo, Xudong Yang, Chengwen Liu, Zhifeng Jing, Juhoon Lee, Matthew Harger, Ally K. Smith, Miguel Espinoza, Hou-Fu Guo, Jonathan M. Kurie, Kevin N. Dalby, Pengyu Y. Ren, G. Andrés Cisneros:
Computational Investigation of a Series of Small Molecules as Potential Compounds for Lysyl Hydroxylase-2 (LH2) Inhibition. 986-1001 - Saikat Pal, Amit Kumar, Harish Vashisth:
Role of Dynamics and Mutations in Interactions of a Zinc Finger Antiviral Protein with CG-rich Viral RNA. 1002-1011 - Adam Stasiulewicz, Anna Lesniak, Magdalena Bujalska-Zadrozny, Tomasz Pawinski, Joanna I. Sulkowska:
Identification of Novel CB2 Ligands through Virtual Screening and In Vitro Evaluation. 1012-1027 - Horrick Sharma, Pragya Sharma, Uzziah Urquiza, Lerin R. Chastain, Michael A. Ihnat:
Exploration of a Large Virtual Chemical Space: Identification of Potent Inhibitors of Lactate Dehydrogenase-A against Pancreatic Cancer. 1028-1043 - Jun Hu, Wen-Wu Zeng, Ning-Xin Jia, Muhammad Arif, Dong-Jun Yu, Gui-Jun Zhang:
Improving DNA-Binding Protein Prediction Using Three-Part Sequence-Order Feature Extraction and a Deep Neural Network Algorithm. 1044-1057 - Kai Kang, Lei Wang, Chen Song:
ProtRAP: Predicting Lipid Accessibility Together with Solvent Accessibility of Proteins in One Run. 1058-1065 - Ran Liu, Xiang Liu, Jie Wu:
Persistent Path-Spectral (PPS) Based Machine Learning for Protein-Ligand Binding Affinity Prediction. 1066-1075 - Xue-Qiang Fan, Bing Lin, Jun Hu, Zhong-Yi Guo:
I-DNAN6mA: Accurate Identification of DNA N6-Methyladenine Sites Using the Base-Pairing Map and Deep Learning. 1076-1086
Volume 63, Number 4, February 2023
- Darya Stepanenko, Stephanie Budhan, Carlos Simmerling:
SpikeScape: A Tool for Analyzing Structural Diversity in Experimental Structures of the SARS-CoV-2 Spike Glycoprotein. 1087-1092 - Jan-Oliver Felix Kapp-Joswig, Bettina G. Keller:
CommonNNClustering─A Python Package for Generic Common-Nearest-Neighbor Clustering. 1093-1098 - Jonathan G. M. Conn, James W. Carter, Justin J. A. Conn, Vigneshwari Subramanian, Andrew Baxter, Ola Engkvist, Antonio Llinàs, Ekaterina Ratkova, Stephen D. Pickett, James L. McDonagh, David S. Palmer:
Blinded Predictions and Post Hoc Analysis of the Second Solubility Challenge Data: Exploring Training Data and Feature Set Selection for Machine and Deep Learning Models. 1099-1113 - Mohammadamin Tavakoli, Yin Ting T. Chiu, Pierre Baldi, Ann Marie Carlton, David Van Vranken:
RMechDB: A Public Database of Elementary Radical Reaction Steps. 1114-1123 - Sergei A. Evteev, Alexey V. Ereshchenko, Yan A. Ivanenkov:
SiteRadar: Utilizing Graph Machine Learning for Precise Mapping of Protein-Ligand-Binding Sites. 1124-1132 - Jintu Zhang, Haotian Zhang, Zhixin Qin, Yu Kang, Xin Hong, Tingjun Hou:
Quasiclassical Trajectory Simulation as a Protocol to Build Locally Accurate Machine Learning Potentials. 1133-1142 - Jiali Guo, Ming Sun, Xueyan Zhao, Chaojie Shi, Haoming Su, Yanzhi Guo, Xuemei Pu:
General Graph Neural Network-Based Model To Accurately Predict Cocrystal Density and Insight from Data Quality and Feature Representation. 1143-1156 - José Manuel Vásquez-Pérez, Luis Ángel Zárate-Hernández, Carlos Zepactonal Gómez-Castro, Uriel Alejandro Nolasco-Hernández:
A Practical Algorithm to Solve the Near-Congruence Problem for Rigid Molecules and Clusters. 1157-1165 - Benjamin I. Tingle, Khanh G. Tang, Mar Castanon, John J. Gutierrez, Munkhzul Khurelbaatar, Chinzorig Dandarchuluun, Yurii S. Moroz, John J. Irwin:
ZINC-22─A Free Multi-Billion-Scale Database of Tangible Compounds for Ligand Discovery. 1166-1176 - Mengxian Yu, Yajuan Shi, Qingzhu Jia, Qiang Wang, Zheng-Hong Luo, Fangyou Yan, Yin-Ning Zhou:
Ring Repeating Unit: An Upgraded Structure Representation of Linear Condensation Polymers for Property Prediction. 1177-1187 - Bumjoon Seo, Brett M. Savoie:
Evidence That Less Can Be More for Transferable Force Fields. 1188-1195 - Zoe Li, Kevin C. Chan, Jonathan D. Nickels, Xiaolin Cheng:
Molecular Dynamics Refinement of Open State Serotonin 5-HT3A Receptor Structures. 1196-1207 - Sara Gómez, Piero Lafiosca, Franco Egidi, Tommaso Giovannini, Chiara Cappelli:
UV-Resonance Raman Spectra of Systems in Complex Environments: A Multiscale Modeling Applied to Doxorubicin Intercalated into DNA. 1208-1217 - Brad Crawford, Umesh Timalsina, Co D. Quach, Nicholas C. Craven, Justin B. Gilmer, Clare McCabe, Peter T. Cummings, Jeffrey J. Potoff:
MoSDeF-GOMC: Python Software for the Creation of Scientific Workflows for the Monte Carlo Simulation Engine GOMC. 1218-1228 - Lokesh Baweja, Jeff Wereszczynski:
Conformational and Thermodynamic Differences Underlying Wild-Type and Mutant Eleven-Nineteen-Leukemia YEATS Domain Specificity for Epigenetic Marks.