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ORCIDJournal of Chemical Information and Modeling, Volume 57
Volume 57, Number 1, January 2017
- G. Goret, B. Aoun, Eric Pellegrini
:
MDANSE: An Interactive Analysis Environment for Molecular Dynamics Simulations. 1-5 - Riccardo Capelli, Filippo Marchetti, Guido Tiana, Giorgio Colombo:
SAGE: A Fast Computational Tool for Linear Epitope Grafting onto a Foreign Protein Scaffold. 6-10
- Florbela Pereira, Kaixia Xiao, Diogo A. R. S. Latino, Chengcheng Wu, Qing-You Zhang, João Aires-de-Sousa:
Machine Learning Methods to Predict Density Functional Theory B3LYP Energies of HOMO and LUMO Orbitals. 11-21 - Qian Zhang, Zhijian Xu, Weiliang Zhu:
The Underestimated Halogen Bonds Forming with Protein Side Chains in Drug Discovery and Design. 22-26
- N. Yi Mok, Nathan Brown:
Applications of Systematic Molecular Scaffold Enumeration to Enrich Structure-Activity Relationship Information. 27-35 - Qingda Zang, Kamel Mansouri, Antony J. Williams, Richard S. Judson, David G. Allen, Warren M. Casey, Nicole C. Kleinstreuer:
In Silico Prediction of Physicochemical Properties of Environmental Chemicals Using Molecular Fingerprints and Machine Learning. 36-49 - Fenglei Cao, Joshua D. Deetz, Huai Sun:
Free Energy-Based Coarse-Grained Force Field for Binary Mixtures of Hydrocarbons, Nitrogen, Oxygen, and Carbon Dioxide. 50-59
- Inês C. M. Simões, Inês P. D. Costa, João T. S. Coimbra, Maria João Ramos, Pedro Alexandrino Fernandes:
New Parameters for Higher Accuracy in the Computation of Binding Free Energy Differences upon Alanine Scanning Mutagenesis on Protein-Protein Interfaces. 60-72 - Prasad Chaskar, Vincent Zoete, Ute F. Röhrig:
On-the-Fly QM/MM Docking with Attracting Cavities. 73-84 - Alfredo Peguero-Tejada, Arjan van der Vaart:
Biasing Simulations of DNA Base Pair Parameters with Application to Propellor Twisting in AT/AT, AA/TT, and AC/GT Steps and Their Uracil Analogs. 85-92
- Nicolas Bosc, Berthold Wroblowski, Christophe Meyer, Pascal Bonnet:
Prediction of Protein Kinase-Ligand Interactions through 2.5D Kinochemometrics. 93-101
- Florent Hédin, Krystel El Hage, Markus Meuwly:
Correction to A Toolkit to Fit Nonbonded Parameters from and for Condensed Phase Simulations. 102-103
Volume 57, Number 2, February 2017
- Stephen J. Capuzzi, Ian Sang-June Kim, Wai In Lam, Thomas E. Thornton, Eugene N. Muratov, Diane Pozefsky, Alexander Tropsha:
Chembench: A Publicly Accessible, Integrated Cheminformatics Portal. 105-108 - Vytautas Gapsys, Bert L. de Groot:
pmx Webserver: A User Friendly Interface for Alchemistry. 109-114 - Ross McGuire, Stefan Verhoeven, Márton Vass, Gerrit Vriend, Iwan J. P. de Esch, Scott J. Lusher, Rob Leurs, Lars Ridder, Albert J. Kooistra, Tina Ritschel, Chris de Graaf:
3D-e-Chem-VM: Structural Cheminformatics Research Infrastructure in a Freely Available Virtual Machine. 115-121 - Florian Flachsenberg, Niek Andresen, Matthias Rarey:
RingDecomposerLib: An Open-Source Implementation of Unique Ring Families and Other Cycle Bases. 122-126
- Adam Pecina, Susanta Haldar, Jindrich Fanfrlík, René Meier, Jan Rezác, Martin Lepsík, Pavel Hobza:
SQM/COSMO Scoring Function at the DFTB3-D3H4 Level: Unique Identification of Native Protein-Ligand Poses. 127-132
- Sabina Podlewska, Wojciech M. Czarnecki, Rafal Kafel, Andrzej J. Bojarski:
Creating the New from the Old: Combinatorial Libraries Generation with Machine-Learning-Based Compound Structure Optimization. 133-147 - Therese Inhester, Stefan Bietz, Matthias Hilbig, Robert Schmidt, Matthias Rarey:
Index-Based Searching of Interaction Patterns in Large Collections of Protein-Ligand Interfaces. 148-158
- Donatella Callegari, Alessio Lodola, Daniele Pala, Silvia Rivara, Marco Mor, Andrea Rizzi, Anna Maria Capelli:
Metadynamics Simulations Distinguish Short- and Long-Residence-Time Inhibitors of Cyclin-Dependent Kinase 8. 159-169 - Ido Y. Ben-Shalom, Stefania Pfeiffer-Marek, Karl-Heinz Baringhaus, Holger Gohlke:
Efficient Approximation of Ligand Rotational and Translational Entropy Changes upon Binding for Use in MM-PBSA Calculations. 170-189 - Hiba Alogheli, Gustav Olanders, Wesley Schaal, Peter Brandt, Anders Karlén:
Docking of Macrocycles: Comparing Rigid and Flexible Docking in Glide. 190-202 - Masaki Matsuoka, Ashutosh Kumar, Muhammad Muddassar, Akihisa Matsuyama, Minoru Yoshida, Kam Y. J. Zhang:
Discovery of Fungal Denitrification Inhibitors by Targeting Copper Nitrite Reductase from Fusarium oxysporum. 203-213 - Yuwei Zhang, Zexing Cao, John Zenghui Zhang, Fei Xia:
Performance Comparison of Systematic Methods for Rigorous Definition of Coarse-Grained Sites of Large Biomolecules. 214-222
- Maxime Melikian, Baptiste Eluard, Gildas Bertho, Véronique Baud, Nathalie Evrard-Todeschi:
Model of the Interaction between the NF-κB Inhibitory Protein p100 and the E3 Ubiquitin Ligase β-TrCP based on NMR and Docking Experiments. 223-233 - Jenny Pirillo, Gloria Mazzone, Nino Russo, Luca Bertini:
Photophysical Properties of S, Se and Te-Substituted Deoxyguanosines: Insight into Their Ability To Act as Chemotherapeutic Agents. 234-242 - Christine Groß, Kay Hamacher, Katja Schmitz, Sven Jager:
Cleavage Product Accumulation Decreases the Activity of Cutinase during PET Hydrolysis. 243-255 - Pedro R. Magalhães, A. Sofia F. Oliveira, Sara R. R. Campos, Cláudio M. Soares, António M. Baptista:
Effect of a pH Gradient on the Protonation States of Cytochrome c Oxidase: A Continuum Electrostatics Study. 256-266 - Ya Gao, Chaomin Zhang, John Z. H. Zhang, Ye Mei:
Evaluation of the Coupled Two-Dimensional Main Chain Torsional Potential in Modeling Intrinsically Disordered Proteins. 267-274 - Marie Zgarbová, Petr Jurecka, Filip Lankas, Thomas E. Cheatham III, Jirí Sponer, Michal Otyepka:
Influence of BII Backbone Substates on DNA Twist: A Unified View and Comparison of Simulation and Experiment for All 136 Distinct Tetranucleotide Sequences. 275-287 - Xukai Jiang, Wen Li, Guanjun Chen, Lushan Wang:
Dynamic Perturbation of the Active Site Determines Reversible Thermal Inactivation in Glycoside Hydrolase Family 12. 288-297 - Elke Haensele, Nawel Mele, Marija Miljak, Christopher M. Read, David C. Whitley, Lee Banting, Carla Delépée, Jana Sopkova-de Oliveira Santos, Alban Lepailleur, Ronan Bureau, Jonathan W. Essex, Timothy Clark:
Conformation and Dynamics of Human Urotensin II and Urotensin Related Peptide in Aqueous Solution. 298-310
- Dawid Warszycki, Manuel Rueda, Stefan Mordalski, Kurt Kristiansen, Grzegorz Satala, Krzysztof Rataj, Zdzislaw Chilmonczyk, Ingebrigt Sylte, Ruben Abagyan, Andrzej J. Bojarski:
From Homology Models to a Set of Predictive Binding Pockets-a 5-HT1A Receptor Case Study. 311-321 - Neha Rana, Jason M. Conley, Monica Soto-Velasquez, Francisco León, Stephen J. Cutler, Val J. Watts, Markus A. Lill:
Molecular Modeling Evaluation of the Enantiomers of a Novel Adenylyl Cyclase 2 Inhibitor. 322-334 - Sreya Mukherjee, Aleksandra Karolak, Marjolaine Debant, Paul Buscaglia, Yves Renaudineau, Olivier Mignen, Wayne C. Guida, Wesley H. Brooks:
Molecular Dynamics Simulations of Membrane-Bound STIM1 to Investigate Conformational Changes during STIM1 Activation upon Calcium Release. 335-344 - Michael Schauperl, Paul Czodrowski, Julian E. Fuchs, Roland G. Huber, Birgit J. Waldner, Maren Podewitz, Christian Kramer, Klaus R. Liedl:
Binding Pose Flip Explained via Enthalpic and Entropic Contributions. 345-354 - Chen Zhang, Ling-Jun Feng, Yi-You Huang, Deyan Wu, Zhe Li, Qian Zhou, Yinuo Wu, Hai-Bin Luo:
Discovery of Novel Phosphodiesterase-2A Inhibitors by Structure-Based Virtual Screening, Structural Optimization, and Bioassay. 355-364 - Marcus Wieder, Arthur Garon, Ugo Perricone, Stefan Boresch, Thomas Seidel, Anna Maria Almerico, Thierry Langer:
Common Hits Approach: Combining Pharmacophore Modeling and Molecular Dynamics Simulations. 365-385
- Donatella Callegari, Alessio Lodola, Daniele Pala, Silvia Rivara, Marco Mor, Andrea Rizzi, Anna Maria Capelli:
Correction to Metadynamics Simulations Distinguish Short- and Long-Residence-Time Inhibitors of Cyclin-Dependent Kinase 8. 386
Volume 57, Number 3, March 2017
- Courtney Aldrich, Carolyn R. Bertozzi, Gunda I. Georg, Laura Kiessling, Craig Lindsley, Dennis Liotta, Kenneth M. Merz Jr., Alanna Schepartz, Shaomeng Wang:
The Ecstasy and Agony of Assay Interference Compounds. 387-390
- Federico Zahariev, Nuwan De Silva, Mark S. Gordon, Theresa L. Windus, Marilu Dick-Perez:
ParFit: A Python-Based Object-Oriented Program for Fitting Molecular Mechanics Parameters to ab Initio Data. 391-396 - Mariana González-Medina, Oscar Méndez-Lucio, José L. Medina-Franco:
Activity Landscape Plotter: A Web-Based Application for the Analysis of Structure-Activity Relationships. 397-402
- Weilin Zhang, Jianfeng Pei, Luhua Lai:
Computational Multitarget Drug Design. 403-412
- Malika Kumarasiri, Theodosia Teo, Mingfeng Yu, Stephen Philip, Sunita K. C. Basnet, Hugo Albrecht, Matthew J. Sykes, Peng Wang, Shudong Wang:
In Search of Novel CDK8 Inhibitors by Virtual Screening. 413-416
- Stephen J. Capuzzi, Eugene N. Muratov, Alexander Tropsha:
Phantom PAINS: Problems with the Utility of Alerts for Pan-Assay INterference CompoundS. 417-427 - Arne Wagner, Hans-Jörg Himmel:
aRMSD: A Comprehensive Tool for Structural Analysis. 428-438 - Fredrik Svensson, Ulf Norinder, Andreas Bender:
Improving Screening Efficiency through Iterative Screening Using Docking and Conformal Prediction. 439-444 - Andreas Verras, Chris L. Waller, Peter Gedeck, Darren V. S. Green, Thierry Kogej, Anandkumar Raichurkar, Manoranjan Panda, Anang A. Shelat, Julie Clark, R. Kiplin Guy, George Papadatos, Jeremy N. Burrows:
Shared Consensus Machine Learning Models for Predicting Blood Stage Malaria Inhibition. 445-453 - Joshua Pottel, Nicolas Moitessier:
Customizable Generation of Synthetically Accessible, Local Chemical Subspaces. 454-467 - Xianjun Fu, Lewis H. Mervin, Xuebo Li, Huayun Yu, Jiaoyang Li, Siti Zuraidah Mohamad Zobir, Azedine Zoufir, Yang Zhou, Yongmei Song, Zhenguo Wang, Andreas Bender:
Toward Understanding the Cold, Hot, and Neutral Nature of Chinese Medicines Using in Silico Mode-of-Action Analysis. 468-483 - Junfeng Liu, Xia Ning:
Multi-Assay-Based Compound Prioritization via Assistance Utilization: A Machine Learning Framework. 484-498
- Yuezhou Zhang, Alexandre Borrel, Leo Ghemtio, Leslie Regad, Gustav Boije af Gennäs, Anne-Claude Camproux, Jari Yli-Kauhaluoma, Henri Xhaard:
Structural Isosteres of Phosphate Groups in the Protein Data Bank. 499-516 - Wei Chun Ng, Thong Leng Lim, Tiem Leong Yoon:
Investigation of Melting Dynamics of Hafnium Clusters. 517-528 - Nils-Ole Friedrich, Agnes Meyder, Christina de Bruyn Kops, Kai Sommer, Florian Flachsenberg, Matthias Rarey, Johannes Kirchmair:
High-Quality Dataset of Protein-Bound Ligand Conformations and Its Application to Benchmarking Conformer Ensemble Generators. 529-539 - Gabriela L. Borosky:
Quantum-Mechanical Study on the Catalytic Mechanism of Alkaline Phosphatases. 540-549
- Diego E. Escalante, Kelly G. Aukema, Lawrence P. Wackett, Alptekin Aksan:
Simulation of the Bottleneck Controlling Access into a Rieske Active Site: Predicting Substrates of Naphthalene 1, 2-Dioxygenase. 550-561 - Bartholomé Delort, Pedro Renault, Landry Charlier, Florent Raussin, Jean Martinez, Nicolas Floquet:
Coarse-Grained Prediction of Peptide Binding to G-Protein Coupled Receptors. 562-571 - Piyanat Meekrathok, Predrag Kukic, Jens Erik Nielsen, Wipa Suginta:
Investigation of Ionization Pattern of the Adjacent Acidic Residues in the DXDXE Motif of GH-18 Chitinases Using Theoretical pKa Calculations. 572-583 - Théau Debroise, Eugene I. Shakhnovich, Nicolas Chéron:
A Hybrid Knowledge-Based and Empirical Scoring Function for Protein-Ligand Interaction: SMoG2016. 584-593
- Naeem Shaikh, Mahesh Sharma, Prabha Garg:
Selective Fusion of Heterogeneous Classifiers for Predicting Substrates of Membrane Transporters. 594-607 - Eleni Kotsampasakou, Gerhard F. Ecker:
Predicting Drug-Induced Cholestasis with the Help of Hepatic Transporters - An in Silico Modeling Approach. 608-615 - Hanwen Du, Junhao Li, Yingchun Cai, Hongxiao Zhang, Guixia Liu, Yun Tang, Weihua Li:
Computational Investigation of Ligand Binding to the Peripheral Site in CYP3A4: Conformational Dynamics and Inhibitor Discovery. 616-626
Volume 57, Number 4, April 2017
- Tairan Liu, Misagh Naderi, Chris Alvin, Supratik Mukhopadhyay, Michal Brylinski:
Break Down in Order To Build Up: Decomposing Small Molecules for Fragment-Based Drug Design with eMolFrag. 627-631 - Masaaki Matsubara, Kiyoko F. Aoki-Kinoshita, Nobuyuki P. Aoki, Issaku Yamada, Hisashi Narimatsu:
WURCS 2.0 Update To Encapsulate Ambiguous Carbohydrate Structures. 632-637 - Anastasia V. Rudik, Vladislav M. Bezhentsev, Alexander V. Dmitriev, Dmitry S. Druzhilovskiy, Alexey Lagunin, Dmitry Filimonov, Vladimir Poroikov:
MetaTox: Web Application for Predicting Structure and Toxicity of Xenobiotics' Metabolites. 638-642 - Mahendra Awale, Daniel Probst, Jean-Louis Reymond:
WebMolCS: A Web-Based Interface for Visualizing Molecules in Three-Dimensional Chemical Spaces. 643-649 - James A. Graham, Jonathan W. Essex, Syma Khalid:
PyCGTOOL: Automated Generation of Coarse-Grained Molecular Dynamics Models from Atomistic Trajectories. 650-656
- Sungjin Kim, Adrian Jinich, Alán Aspuru-Guzik:
MultiDK: A Multiple Descriptor Multiple Kernel Approach for Molecular Discovery and Its Application to Organic Flow Battery Electrolytes. 657-668 - Shenzhen Huang, Chunli Song, Xiang Wang, Guo Zhang, Yanlin Wang, Xiaojuan Jiang, Qizheng Sun, Luyi Huang, Rong Xiang, Yiguo Hu, Linli Li, Sheng-Yong Yang:
Discovery of New SIRT2 Inhibitors by Utilizing a Consensus Docking/Scoring Strategy and Structure-Activity Relationship Analysis. 669-679 - Aleksejs Kontijevskis:
Mapping of Drug-like Chemical Universe with Reduced Complexity Molecular Frameworks. 680-699 - Ricardo Visini, Mahendra Awale, Jean-Louis Reymond:
Fragment Database FDB-17. 700-709 - Raquel Rodríguez-Pérez, Martin Vogt, Jürgen Bajorath:
Influence of Varying Training Set Composition and Size on Support Vector Machine-Based Prediction of Active Compounds. 710-716
- Silvia Rinaldi, Alessandro Gori, Celeste Annovazzi, Erica E. Ferrandi, Daniela Monti, Giorgio Colombo:
Unraveling Energy and Dynamics Determinants to Interpret Protein Functional Plasticity: The Limonene-1, 2-epoxide-hydrolase Case Study. 717-725 - Sereina Riniker:
Molecular Dynamics Fingerprints (MDFP): Machine Learning from MD Data To Predict Free-Energy Differences. 726-741 - Shota Uehara, Shigenori Tanaka:
Cosolvent-Based Molecular Dynamics for Ensemble Docking: Practical Method for Generating Druggable Protein Conformations. 742-756
- Dóra K. Menyhárd, Ilona Hudáky, Imre Jákli, György Juhász, András Perczel:
Predictable Conformational Diversity in Foldamers of Sugar Amino Acids. 757-768 - Inès Rasolohery, Gautier Moroy, Frédéric Guyon:
PatchSearch: A Fast Computational Method for Off-Target Detection. 769-777 - Wasinee Khuntawee, Manaschai Kunaseth, Chompoonut Rungnim, Suradej Intagorn, Peter Wolschann, Nawee Kungwan, Thanyada Rungrotmongkol, Supot Hannongbua:
Comparison of Implicit and Explicit Solvation Models for Iota-Cyclodextrin Conformation Analysis from Replica Exchange Molecular Dynamics. 778-786 - Milan Mladenovic, Alexandros Patsilinakos, Adele Pirolli, Manuela Sabatino, Rino Ragno:
Understanding the Molecular Determinant of Reversible Human Monoamine Oxidase B Inhibitors Containing 2H-Chromen-2-One Core: Structure-Based and Ligand-Based Derived Three-Dimensional Quantitative Structure-Activity Relationships Predictive Models. 787-814 - Pragati Agnihotri, Arjun K. Mishra, Shikha Mishra, Vijay Kumar Sirohi, Amogh A. Sahasrabuddhe, J. Venkatesh Pratap:
Identification of Novel Inhibitors of Leishmania donovani γ-Glutamylcysteine Synthetase Using Structure-Based Virtual Screening, Docking, Molecular Dynamics Simulation, and in Vitro Studies. 815-825 - Rodrigo Cossio-Pérez, Juliana Palma, Gustavo Pierdominici-Sottile:
Consistent Principal Component Modes from Molecular Dynamics Simulations of Proteins. 826-834 - Zhengya Bai, Shasha Hou, Shilei Zhang, Zhongyan Li, Peng Zhou:
Targeting Self-Binding Peptides as a Novel Strategy To Regulate Protein Activity and Function: A Case Study on the Proto-oncogene Tyrosine Protein Kinase c-Src. 835-845 - Juan Pablo Arcon, Lucas A. Defelipe, Carlos P. Modenutti, Elias D. López, Daniel Alvarez-Garcia, Xavier Barril, Adrian Gustavo Turjanski, Marcelo A. Marti:
Molecular Dynamics in Mixed Solvents Reveals Protein-Ligand Interactions, Improves Docking, and Allows Accurate Binding Free Energy Predictions. 846-863 - Kevin Hauser, Yiqing He, Miguel Garcia-Diaz, Carlos Simmerling, Evangelos A. Coutsias:
Characterization of Biomolecular Helices and Their Complementarity Using Geometric Analysis. 864-874 - William Yuan, Dadi Jiang, Dhanya K. Nambiar, Lydia P. Liew, Michael P. Hay, Joshua Bloomstein, Peter Lu, Brandon Turner, Quynh-Thu Le, Robert Tibshirani, Purvesh Khatri, Mark G. Moloney, Albert C. Koong:
Chemical Space Mimicry for Drug Discovery. 875-882 - S. Harikrishna, P. I. Pradeepkumar:
Probing the Binding Interactions between Chemically Modified siRNAs and Human Argonaute 2 Using Microsecond Molecular Dynamics Simulations. 883-896 - Shunzhou Wan, Agastya Bhati, Sarah Skerratt, Kiyoyuki Omoto, Veerabahu Shanmugasundaram, Sharan K. Bagal, Peter V. Coveney:
Evaluation and Characterization of Trk Kinase Inhibitors for the Treatment of Pain: Reliable Binding Affinity Predictions from Theory and Computation. 897-909 - Zoltan Antal, Janos Szoverfi, Szilard N. Fejer:
Predicting the Initial Steps of Salt-Stable Cowpea Chlorotic Mottle Virus Capsid Assembly with Atomistic Force Fields. 910-917 - Guodong Hu, Aijing Ma, Jihua Wang:
Ligand Selectivity Mechanism and Conformational Changes in Guanine Riboswitch by Molecular Dynamics Simulations and Free Energy Calculations. 918-928
- Majid Jafari, Faramarz Mehrnejad, Raheleh Aghdami, Nader Chaparzadeh, Zahra Razaghi Moghadam Kashani, Farahnoosh Doustdar:
Identification of the Crucial Residues in the Early Insertion of Pardaxin into Different Phospholipid Bilayers. 929-941 - Matthew Ragoza, Joshua E. Hochuli, Elisa Idrobo, Jocelyn Sunseri, David Ryan Koes:
Protein-Ligand Scoring with Convolutional Neural Networks. 942-957 - Érica Cristina Moreno Nascimento, Mónica Oliva, Katarzyna Swiderek, João Batista Lopes Martins, Juan Andrés:
Binding Analysis of Some Classical Acetylcholinesterase Inhibitors: Insights for a Rational Design Using Free Energy Perturbation Method Calculations with QM/MM MD Simulations. 958-976 - Yuan-xin Tian, Yonghuan Yu, Yudong Shen, Hua Wan, Shan Chang, Tingting Zhang, Shanhe Wan, Jiajie Zhang:
Molecular Simulation Studies on the Binding Selectivity of Type-I Inhibitors in the Complexes with ROS1 versus ALK. 977-987
- Yi-Ze Zhang, Hong-Bin Shen:
Signal-3L 2.0: A Hierarchical Mixture Model for Enhancing Protein Signal Peptide Prediction by Incorporating Residue-Domain Cross-Level Features. 988-999 - Leihong Wu, Zhichao Liu, Scott M. Auerbach, Ruili Huang, Minjun Chen, Kristin McEuen, Joshua Xu, Hong Fang, Weida Tong:
Integrating Drug's Mode of Action into Quantitative Structure-Activity Relationships for Improved Prediction of Drug-Induced Liver Injury. 1000-1006 - Yang Li, Jianyi Yang:
Structural and Sequence Similarity Makes a Significant Impact on Machine-Learning-Based Scoring Functions for Protein-Ligand Interactions. 1007-1012
Volume 57, Number 5, May 2017
- Rodolpho C. Braga, Vinicius M. Alves, Eugene N. Muratov, Judy Strickland, Nicole C. Kleinstreuer, Alexander Tropsha, Carolina Horta Andrade:
Pred-Skin: A Fast and Reliable Web Application to Assess Skin Sensitization Effect of Chemicals. 1013-1017
- Fuqiang Ban, Kush Dalal, Huifang Li, Eric Leblanc, Paul S. Rennie, Artem Cherkasov:
Best Practices of Computer-Aided Drug Discovery: Lessons Learned from the Development of a Preclinical Candidate for Prostate Cancer with a New Mechanism of Action. 1018-1028
- Michael González-Durruthy, Luciane C. Alberici, Carlos Curti, Zeki Naal, David T. Atique-Sawazaki, José Manuel Vázquez-Naya, Humberto González Díaz, Cristian R. Munteanu:
Experimental-Computational Study of Carbon Nanotube Effects on Mitochondrial Respiration: In Silico Nano-QSPR Machine Learning Models Based on New Raman Spectra Transform with Markov-Shannon Entropy Invariants. 1029-1044 - Berhane Temelso, Joel M. Mabey, Toshiro Kubota, Nana Appiah-Padi, George C. Shields:
ArbAlign: A Tool for Optimal Alignment of Arbitrarily Ordered Isomers Using the Kuhn-Munkres Algorithm. 1045-1054 - Ying Dong, Bingren Xiang, Ding Du:
PVLOO-Based Training Set Selection Improves the External Predictability of QSAR/QSPR Models. 1055-1067
- Seungryong Heo, Juyong Lee, Keehyoung Joo, Hang-Cheol Shin, Jooyoung Lee:
Protein Loop Structure Prediction Using Conformational Space Annealing. 1068-1078 - Tingting Zhang, Gaurav Sharma, Thomas J. Paul, Zachary Hoffmann, Rajeev Prabhakar:
Effects of Ligand Environment in Zr(IV) Assisted Peptide Hydrolysis. 1079-1088 - Xin Wang, Fu-Quan Bai, Yingtao Liu, Yu Wang, Hong-Xing Zhang, Zhenyang Lin:
A Computational Way To Achieve More Effective Candidates for Photodynamic Therapy. 1089-1100
- Si Chen, Zhiwei Feng, Yun Wang, Shifan Ma, Ziheng Hu, Peng Yang, Yifeng Chai, Xiang-Qun Xie:
Discovery of Novel Ligands for TNF-α and TNF Receptor-1 through Structure-Based Virtual Screening and Biological Assay. 1101-1111 - Yuna Yan, Maoyou Yang, Chang G. Ji, John Z. H. Zhang:
Interaction Entropy for Computational Alanine Scanning. 1112-1122 - Silvia Bonomo, Flemming Steen Jørgensen, Lars Olsen:
Mechanism of Cytochrome P450 17A1-Catalyzed Hydroxylase and Lyase Reactions. 1123-1133 - Hao Sha, Fangqiang Zhu:
Parameter Optimization for Interaction between C-Terminal Domains of HIV-1 Capsid Protein. 1134-1141 - Georgios Iakovou, Steven Hayward, Stephen D. Laycock:
Virtual Environment for Studying the Docking Interactions of Rigid Biomolecules with Haptics. 1142-1152 - Wei Ye, Tianle Qian, Hao Liu, Ray Luo, Hai-Feng Chen:
Allosteric Autoinhibition Pathway in Transcription Factor ERG: Dynamics Network and Mutant Experimental Evaluations. 1153-1165 - Dong Song, Ray Luo, Hai-Feng Chen:
The IDP-Specific Force Field ff14IDPSFF Improves the Conformer Sampling of Intrinsically Disordered Proteins. 1166-1178 - Jianzhuang Yao, Haixia Luo, Xia Wang:
Understanding the Catalytic Mechanism and the Substrate Specificity of an Engineered Gluten Hydrolase by QM/MM Molecular Dynamics and Free Energy Simulations. 1179-1186
- Emanuel S. R. Ehmki, Christian Kramer:
Matched Molecular Series: Measuring SAR Similarity. 1187-1196 - Malgorzata N. Drwal, Célien Jacquemard, Carlos Perez, Jérémy Desaphy, Esther Kellenberger:
Do Fragments and Crystallization Additives Bind Similarly to Drug-like Ligands? 1197-1209 - Noureldin Saleh, Passainte Ibrahim, Giorgio Saladino, Francesco L. Gervasio, Timothy Clark:
An Efficient Metadynamics-Based Protocol To Model the Binding Affinity and the Transition State Ensemble of G-Protein-Coupled Receptor Ligands. 1210-1217 - Shilva Kayastha, Dragos Horvath, Erik Gilberg, Michael Gütschow, Jürgen Bajorath, Alexandre Varnek:
Privileged Structural Motif Detection and Analysis Using Generative Topographic Maps. 1218-1232
Volume 57, Number 6, June 2017
- Edward J. Milton, Tianhong Zhang, Claire Bellamy, Gregg Alan Swayze, Christopher Hart, Markus Weisser, Sabrina Hecht, Sergio H. Rotstein:
HELM Software for Biopolymers. 1233-1239 - Piero Procacci:
PrimaDORAC: A Free Web Interface for the Assignment of Partial Charges, Chemical Topology, and Bonded Parameters in Organic or Drug Molecules. 1240-1245 - Zahra Dolatkhah, Shahrzad Javanshir, Ahmad Shahir Sadr, Jaber Hosseini, Soroush Sardari:
Synthesis, Molecular Docking, Molecular Dynamics Studies, and Biological Evaluation of 4H-Chromone-1,2,3,4-tetrahydropyrimidine-5-carboxylate Derivatives as Potential Antileukemic Agents. 1246-1257 - Christina de Bruyn Kops, Nils-Ole Friedrich, Johannes Kirchmair:
Alignment-Based Prediction of Sites of Metabolism. 1258-1264 - Benjamin D. Sellers, Natalie C. James, Alberto Gobbi:
A Comparison of Quantum and Molecular Mechanical Methods to Estimate Strain Energy in Druglike Fragments. 1265-1275 - Melissa Coates Ford, Kerim Babaoglu:
Examining the Feasibility of Using Free Energy Perturbation (FEP+) in Predicting Protein Stability. 1276-1285 - Jeremy R. Ash, Denis Fourches:
Characterizing the Chemical Space of ERK2 Kinase Inhibitors Using Descriptors Computed from Molecular Dynamics Trajectories. 1286-1299 - Maho Nakata, Tomomi Shimazaki:
PubChemQC Project: A Large-Scale First-Principles Electronic Structure Database for Data-Driven Chemistry. 1300-1308 - Prashant Joshi, Glen J. P. McCann, Vinay R. Sonawane, Ram A. Vishwakarma, Bhabatosh Chaudhuri, Sandip B. Bharate:
Identification of Potent and Selective CYP1A1 Inhibitors via Combined Ligand and Structure-Based Virtual Screening and Their in Vitro Validation in Sacchrosomes and Live Human Cells. 1309-1320 - Jaroslaw Polanski, Aleksandra Tkocz:
Between Descriptors and Properties: Understanding the Ligand Efficiency Trends for G Protein-Coupled Receptor and Kinase Structure-Activity Data Sets. 1321-1329 - Stephanie Jephthah, João Henriques, Carolina Cragnell, Sumant Puri, Mira Edgerton, Marie Skepö:
Structural Characterization of Histatin 5-Spermidine Conjugates: A Combined Experimental and Theoretical Study. 1330-1341 - Orkid Coskuner, Vladimir N. Uversky:
Tyrosine Regulates β-Sheet Structure Formation in Amyloid-β42: A New Clustering Algorithm for Disordered Proteins. 1342-1358 - David L. Penkler, Özge Sensoy, Canan Atilgan, Özlem Tastan Bishop:
Perturbation-Response Scanning Reveals Key Residues for Allosteric Control in Hsp70. 1359-1374 - Fude Sun, Long Chen, Peng Wei, Mengya Chai, Xiufang Ding, Lida Xu, Shi-Zhong Luo:
Dimerization and Structural Stability of Amyloid Precursor Proteins Affected by the Membrane Microenvironments. 1375-1387 - S. Roy Kimura, Hai Peng Hu, Anatoly M. Ruvinsky, Woody Sherman, Angelo D. Favia:
Deciphering Cryptic Binding Sites on Proteins by Mixed-Solvent Molecular Dynamics. 1388-1401 - Natalia Khuri, Arik A. Zur, Matthias B. Wittwer, Lawrence Lin, Sook Wah Yee, Andrej Sali, Kathleen M. Giacomini:
Computational Discovery and Experimental Validation of Inhibitors of the Human Intestinal Transporter OATP2B1. 1402-1413 - Jie Xia, Jui-Hua Hsieh, Huabin Hu, Song Wu, Xiang Simon Wang:
The Development of Target-Specific Pose Filter Ensembles To Boost Ligand Enrichment for Structure-Based Virtual Screening. 1414-1425 - Xinya Han, Xiuyun Zhu, Zongqin Hong, Lin Wei, Yanliang Ren, Fen Wan, Shuaihua Zhu, Hao Peng, Li Guo, Li Rao, Lingling Feng, Jian Wan:
Structure-Based Rational Design of Novel Inhibitors Against Fructose-1,6-Bisphosphate Aldolase from Candida albicans. 1426-1438 - Yanmin Zhang, Lu Wang, Qing Zhang, Gaoyuan Zhu, Zhimin Zhang, Xiang Zhou, Yadong Chen, Tao Lu, Weifang Tang:
Potent Pan-Raf and Receptor Tyrosine Kinase Inhibitors Based on a Cyclopropyl Formamide Fragment Overcome Resistance. 1439-1452 - Weilin Zhang, Jianfeng Pei, Luhua Lai:
Statistical Analysis and Prediction of Covalent Ligand Targeted Cysteine Residues. 1453-1460 - Shubhadip Das, Sandip Paul:
Hydrotropic Action of Cationic Hydrotrope p-Toluidinium Chloride on the Solubility of Sparingly Soluble Gliclazide Drug Molecule: A Computational Study. 1461-1473 - Sheng Tian, Xu Wang, Linlang Li, Xiaohu Zhang, Youyong Li, Feng Zhu, Tingjun Hou, Xuechu Zhen:
Discovery of Novel and Selective Adenosine A2A Receptor Antagonists for Treating Parkinson's Disease through Comparative Structure-Based Virtual Screening. 1474-1487 - Luca Codutti, Manuela Grimaldi, Teresa Carlomagno:
Structure-Based Design of Scaffolds Targeting PDE10A by INPHARMA-NMR. 1488-1498 - Xiuquan Du, Shiwei Sun, Changlin Hu, Yu Yao, Yuan-Ting Yan, Yanping Zhang:
DeepPPI: Boosting Prediction of Protein-Protein Interactions with Deep Neural Networks. 1499-1510
Volume 57, Number 7, July 2017
- Gerard Martínez-Rosell, Toni Giorgino, Gianni De Fabritiis:
PlayMolecule ProteinPrepare: A Web Application for Protein Preparation for Molecular Dynamics Simulations. 1511-1516 - Wei Xiao, Zenghui He, Meijian Sun, Shiliang Li, Honglin Li:
Statistical Analysis, Investigation, and Prediction of the Water Positions in the Binding Sites of Proteins. 1517-1528 - Qian Zhang, Zhijian Xu, Jiye Shi, Weiliang Zhu:
Underestimated Halogen Bonds Forming with Protein Backbone in Protein Data Bank. 1529-1534 - Suqing Zheng, Shaofang Xu, Guitao Wang, Qing Tang, Xiaonan Jiang, Zhanting Li, Yong Xu, Renxiao Wang, Fu Lin:
Proposed Hydrogen-Bonding Index of Donor or Acceptor Reflecting Its Intrinsic Contribution to Hydrogen-Bonding Strength. 1535-1547 - Kwanghyok Jong, Luca Grisanti, Ali Hassanali:
Hydrogen Bond Networks and Hydrophobic Effects in the Amyloid β30-35 Chain in Water: A Molecular Dynamics Study. 1548-1562 - Stefano Motta, Laura Bonati:
Modeling Binding with Large Conformational Changes: Key Points in Ensemble-Docking Approaches. 1563-1578 - Spencer S. Ericksen, Haozhen Wu, Huikun Zhang, Lauren A. Michael, Michael A. Newton, F. Michael Hoffmann, Scott A. Wildman:
Machine Learning Consensus Scoring Improves Performance Across Targets in Structure-Based Virtual Screening. 1579-1590 - Jiangming Sun, Lars Carlsson, Ernst Ahlberg, Ulf Norinder, Ola Engkvist, Hongming Chen:
Applying Mondrian Cross-Conformal Prediction To Estimate Prediction Confidence on Large Imbalanced Bioactivity Data Sets. 1591-1598 - Zheng Gong, Huai Sun:
A Coarse-Grained Force Field Parameterized for MgCl2 and CaCl2 Aqueous Solutions. 1599-1608 - Yunhui Ge, Brandon L. Kier, Niels H. Andersen, Vincent A. Voelz:
Computational and Experimental Evaluation of Designed β-Cap Hairpins Using Molecular Simulations and Kinetic Network Models. 1609-1620 - Zhaoxi Sun, Xiaohui Wang, Jianing Song:
Extensive Assessment of Various Computational Methods for Aspartate's pKa Shift. 1621-1639 - Guo-Bo Li, Zhu-Jun Yu, Sha Liu, Lu-Yi Huang, Ling-Ling Yang, Christopher T. Lohans, Sheng-Yong Yang:
IFPTarget: A Customized Virtual Target Identification Method Based on Protein-Ligand Interaction Fingerprinting Analyses. 1640-1651 - Stefan Güssregen, Hans Matter, Gerhard Hessler, Evanthia Lionta, Jochen Heil, Stefan M. Kast:
Thermodynamic Characterization of Hydration Sites from Integral Equation-Derived Free Energy Densities: Application to Protein Binding Sites and Ligand Series. 1652-1666 - Liying Zhang, Kjell Johnson, Jeremy Starr, Jared Milbank, Andrew M. Kuhn, Christopher Poss, Robert V. Stanton, Veerabahu Shanmugasundaram:
Novel Methods for Prioritizing "Close-In" Analogs from Structure-Activity Relationship Matrices. 1667-1676 - Jing Xing, Wenchao Lu, Rongfeng Liu, Yulan Wang, Yiqian Xie, Hao Zhang, Zhe Shi, Hao Jiang, Yu-Chih Liu, Kaixian Chen, Hualiang Jiang, Cheng Luo, Mingyue Zheng:
Machine-Learning-Assisted Approach for Discovering Novel Inhibitors Targeting Bromodomain-Containing Protein 4. 1677-1690 - Giulio Vistoli, Angelica Mazzolari, Bernard Testa, Alessandro Pedretti:
Binding Space Concept: A New Approach To Enhance the Reliability of Docking Scores and Its Application to Predicting Butyrylcholinesterase Hydrolytic Activity. 1691-1702 - Thomas C. Schmidt, Per-Olof Eriksson, David Gustafsson, David Cosgrove, Bente Frølund, Jonas Boström:
Discovery and Evaluation of Anti-Fibrinolytic Plasmin Inhibitors Derived from 5-(4-Piperidyl)isoxazol-3-ol (4-PIOL). 1703-1714 - Duc Duy Nguyen, Tian Xiao, Menglun Wang, Guo-Wei Wei:
Rigidity Strengthening: A Mechanism for Protein-Ligand Binding. 1715-1721
Volume 57, Number 8, August 2017
- Esben Jannik Bjerrum, Jan H. Jensen, Jakob L. Tolborg:
pICalculax: Improved Prediction of Isoelectric Point for Modified Peptides. 1723-1727 - Dániel Dudola, Bertalan Kovács, Zoltán Gáspári:
CoNSEnsX+ Webserver for the Analysis of Protein Structural Ensembles Reflecting Experimentally Determined Internal Dynamics. 1728-1734 - Mariana González-Medina, José L. Medina-Franco:
Platform for Unified Molecular Analysis: PUMA. 1735-1740 - Leandro G. Radusky, Sergio Ruiz-Carmona, Carlos P. Modenutti, Xavier Barril, Adrian Gustavo Turjanski, Marcelo A. Marti:
LigQ: A Webserver to Select and Prepare Ligands for Virtual Screening. 1741-1746 - Paul C. D. Hawkins:
Conformation Generation: The State of the Art. 1747-1756 - Connor W. Coley, Regina Barzilay, William H. Green Jr., Tommi S. Jaakkola, Klavs F. Jensen:
Convolutional Embedding of Attributed Molecular Graphs for Physical Property Prediction. 1757-1772 - Richard Marchese Robinson, Anna Palczewska, Jan Palczewski, Nathan J. Kidley:
Comparison of the Predictive Performance and Interpretability of Random Forest and Linear Models on Benchmark Data Sets. 1773-1792 - Yuna Yan, Weijun Wang, Zhaoxi Sun, John Z. H. Zhang, Changge Ji:
Protein-Ligand Empirical Interaction Components for Virtual Screening. 1793-1806 - Andrea Johnston, Rajni Bhardwaj-Miglani, Rajesh Gurung, Antony D. Vassileiou, Alastair J. Florence, Blair F. Johnston:
Combined Chemoinformatics Approach to Solvent Library Design Using clusterSim and Multidimensional Scaling. 1807-1815 - Nadine Schneider, Nikolas Fechner, Gregory A. Landrum, Nikolaus Stiefl:
Chemical Topic Modeling: Exploring Molecular Data Sets Using a Common Text-Mining Approach. 1816-1831 - Martin Sícho, Christina de Bruyn Kops, Conrad Stork, Daniel Svozil, Johannes Kirchmair:
FAME 2: Simple and Effective Machine Learning Model of Cytochrome P450 Regioselectivity. 1832-1846 - Peter Gedeck, Suzanne Skolnik, Stephane Rodde:
Developing Collaborative QSAR Models Without Sharing Structures. 1847-1858 - Stefano E. Rensi, Russ B. Altman:
Shallow Representation Learning via Kernel PCA Improves QSAR Modelability. 1859-1867 - Melisa E. Gantner, Roxana N. Peroni, Juan F. Morales, María L. Villalba, María E. Ruiz, Alan Talevi:
Development and Validation of a Computational Model Ensemble for the Early Detection of BCRP/ABCG2 Substrates during the Drug Design Stage. 1868-1880 - Daniel J. Sindhikara, Steven A. Spronk, Tyler Day, Kenneth W. Borrelli, Daniel L. Cheney, Shana L. Posy:
Improving Accuracy, Diversity, and Speed with Prime Macrocycle Conformational Sampling. 1881-1894 - Huiyong Sun, Youyong Li, Mingyun Shen, Dan Li, Yu Kang, Tingjun Hou:
Characterizing Drug-Target Residence Time with Metadynamics: How To Achieve Dissociation Rate Efficiently without Losing Accuracy against Time-Consuming Approaches. 1895-1906 - Heike Thomas, Matthias Hennemann, Patrick Kibies, Franziska Hoffgaard, Stefan Güssregen, Gerhard Hessler, Stefan M. Kast, Timothy Clark:
The hpCADD NDDO Hamiltonian: Parametrization. 1907-1922 - Oliver T. Unke, Markus Meuwly:
Toolkit for the Construction of Reproducing Kernel-Based Representations of Data: Application to Multidimensional Potential Energy Surfaces. 1923-1931 - Luba Simhaev, Nael A. McCarty, Robert C. Ford, Hanoch Senderowitz:
Molecular Dynamics Flexible Fitting Simulations Identify New Models of the Closed State of the Cystic Fibrosis Transmembrane Conductance Regulator Protein. 1932-1946 - Qianyun Ma, Han-Shen Tae, Guanzhao Wu, Tao Jiang, Rilei Yu:
Exploring the Relationship between Nicotinic Acetylcholine Receptor Ligand Size, Efficiency, Efficacy, and C-Loop Opening. 1947-1956 - Priya Mahajan, Gousia Chashoo, Monika Gupta, Amit Kumar, Parvinder Pal Singh, Amit Nargotra:
Fusion of Structure and Ligand Based Methods for Identification of Novel CDK2 Inhibitors. 1957-1969 - Sérgio M. Marques, Zuzana Dunajova, Zbynek Prokop, Radka Chaloupkova, Jan Brezovsky, Jirí Damborský:
Catalytic Cycle of Haloalkane Dehalogenases Toward Unnatural Substrates Explored by Computational Modeling. 1970-1989 - Cory M. Ayres, Timothy P. Riley, Steven A. Corcelli, Brian M. Baker:
Modeling Sequence-Dependent Peptide Fluctuations in Immunologic Recognition. 1990-1998 - Ekaterina D. Kots, Sofya V. Lushchekina, Sergey D. Varfolomeev, Alexander V. Nemukhin:
Role of Protein Dimeric Interface in Allosteric Inhibition of N-Acetyl-Aspartate Hydrolysis by Human Aspartoacylase. 1999-2008 - Amin Reza Zolghadr, Maryam Heydari Dokoohaki:
How Does the P7C3-Series of Neuroprotective Small Molecules Prevent Membrane Disruption? 2009-2019 - Ning Ma, Arjan van der Vaart:
Free Energy Coupling between DNA Bending and Base Flipping. 2020-2026 - Kishore Gajula, Rakesh Gupta, D. B. Sridhar, Beena Rai:
In-Silico Skin Model: A Multiscale Simulation Study of Drug Transport. 2027-2034 - Aby A. Thyparambil, Tigran M. Abramyan, Ingrid Bazin, Anthony Guiseppi-Elie:
Site of Tagging Influences the Ochratoxin Recognition by Peptide NFO4: A Molecular Dynamics Study. 2035-2044 - Dimas Suárez, Natalia Díaz:
Ligand Strain and Entropic Effects on the Binding of Macrocyclic and Linear Inhibitors: Molecular Modeling of Penicillopepsin Complexes. 2045-2055 - Menyhárt-Botond Sárosi, Wilma Neumann, Terry P. Lybrand, Evamarie Hey-Hawkins:
Molecular Modeling of the Interactions between Carborane-Containing Analogs of Indomethacin and Cyclooxygenase-2. 2056-2067 - Bharath Ramsundar, Bowen Liu, Zhenqin Wu, Andreas Verras, Matthew Tudor, Robert P. Sheridan, Vijay S. Pande:
Is Multitask Deep Learning Practical for Pharma? 2068-2076 - Eric J. Martin, Valery R. Polyakov, Li Tian, Rolando C. Perez:
Profile-QSAR 2.0: Kinase Virtual Screening Accuracy Comparable to Four-Concentration IC50s for Realistically Novel Compounds. 2077-2088 - Martin Kotev, Pilar Manuel-Manresa, Elsa Hernando, Vanessa Soto-Cerrato, Modesto Orozco, Roberto Quesada, Ricardo Pérez-Tomás, Victor Guallar:
Inhibition of Human Enhancer of Zeste Homolog 2 with Tambjamine Analogs. 2089-2098
Volume 57, Number 9, September 2017
- Ya Chen, Christina de Bruyn Kops, Johannes Kirchmair:
Data Resources for the Computer-Guided Discovery of Bioactive Natural Products. 2099-2111 - Davide Sala, Silvia Ciambellotti, Andrea Giachetti, Paola Turano, Antonio Rosato:
Investigation of the Iron(II) Release Mechanism of Human H-Ferritin as a Function of pH. 2112-2118 - Julia Nogueira Varela, María Fernanda Lammoglia Cobo, Sandip V. Pawar, Vikramaditya G. Yadav:
Cheminformatic Analysis of Antimalarial Chemical Space Illuminates Therapeutic Mechanisms and Offers Strategies for Therapy Development. 2119-2131 - Therese Inhester, Eva Nittinger, Kai Sommer, Pascal Schmidt, Stefan Bietz, Matthias Rarey:
NAOMInova: Interactive Geometric Analysis of Noncovalent Interactions in Macromolecular Structures. 2132-2142 - Víctor Sebastián-Pérez, Carlos Roca, Mahendra Awale, Jean-Louis Reymond, Ana Martínez, Carmen Gil, Nuria E. Campillo:
Medicinal and Biological Chemistry (MBC) Library: An Efficient Source of New Hits. 2143-2151 - Prasenjit Mukherjee, Jörg Bentzien, Todd Bosanac, Wang Mao, Michael Burke, Ingo Muegge:
Kinase Crystal Miner: A Powerful Approach to Repurposing 3D Hinge Binding Fragments and Its Application to Finding Novel Bruton Tyrosine Kinase Inhibitors. 2152-2160 - Charalampos Chomenidis, Georgios Drakakis, Georgia Tsiliki, Evangelia Anagnostopoulou, Angelos Valsamis, Philip Doganis, Pantelis Sopasakis, Haralambos Sarimveis:
Jaqpot Quattro: A Novel Computational Web Platform for Modeling and Analysis in Nanoinformatics. 2161-2172 - Jean-Patrick Francoia, Jean-Christophe Rossi, Gerald Monard, Laurent Vial:
Digitizing Poly-l-lysine Dendrigrafts: From Experimental Data to Molecular Dynamics Simulations. 2173-2180 - Denys E. S. Santos, Laercio Pol-Fachin, Roberto D. Lins, Thereza A. Soares:
Polymyxin Binding to the Bacterial Outer Membrane Reveals Cation Displacement and Increasing Membrane Curvature in Susceptible but Not in Resistant Lipopolysaccharide Chemotypes. 2181-2193 - Ruifeng Liu, Mohamed Diwan M. AbdulHameed, Anders Wallqvist:
Molecular Structure-Based Large-Scale Prediction of Chemical-Induced Gene Expression Changes. 2194-2202 - Matteo Aldeghi, Michael J. Bodkin, Stefan Knapp, Philip C. Biggin:
Statistical Analysis on the Performance of Molecular Mechanics Poisson-Boltzmann Surface Area versus Absolute Binding Free Energy Calculations: Bromodomains as a Case Study. 2203-2221 - Aysegül Turupcu, Chris Oostenbrink:
Modeling of Oligosaccharides within Glycoproteins from Free-Energy Landscapes. 2222-2236 - Mary Varughese, P. Haris, Mathew K. Varghese, P. Aparna, C. Sudarsanakumar:
Experimental Probing and Molecular Dynamics Simulation of the Molecular Recognition of DNA Duplexes by the Flavonoid Luteolin. 2237-2249 - David Xu, Yubing Si, Samy O. Meroueh:
A Computational Investigation of Small-Molecule Engagement of Hot Spots at Protein-Protein Interaction Interfaces. 2250-2272 - Jinfeng Huang, Bin Sun, Yuan Yao, Junjun Liu:
Fast and Reliable Thermodynamic Approach for Determining the Protonation State of the Asp Dyad. 2273-2280 - Tingting Zhang, Yuan-xin Tian, Zhonghuang Li, Siming Liu, Xiang Hu, Zichao Yang, Xiaotong Ling, Shuwen Liu, Jiajie Zhang:
Molecular Dynamics Study to Investigate the Dimeric Structure of the Full-Length α-Synuclein in Aqueous Solution. 2281-2293 - Marc van Dijk, Antonius ter Laak, Jörg D. Wichard, Luigi Capoferri, Nico P. E. Vermeulen, Daan P. Geerke:
Comprehensive and Automated Linear Interaction Energy Based Binding-Affinity Prediction for Multifarious Cytochrome P450 Aromatase Inhibitors. 2294-2308 - Jingwei Zhou, Yue Huang, Chunyan Cheng, Kai Wang, Ruibo Wu:
Intrinsic Dynamics of the Binding Rail and Its Allosteric Effect in the Class I Histone Deacetylases. 2309-2320 - Amit Kumar, Debadrita Basu, Priyadarshi Satpati:
Structure-Based Energetics of Stop Codon Recognition by Eukaryotic Release Factor. 2321-2328 - Haiyan Cai, Ting Wang, Zhuo Yang, Zhijian Xu, Guimin Wang, He-Yao Wang, Weiliang Zhu, Kaixian Chen:
Combined Virtual Screening and Substructure Search for Discovery of Novel FABP4 Inhibitors. 2329-2335 - Yan Wang, Huang-Quan Lin, Ping Wang, Jian-Shu Hu, Tsz-Ming Ip, Liu-Meng Yang, Yong-Tang Zheng, David Chi-Cheong Wan:
Discovery of a Novel HIV-1 Integrase/p75 Interacting Inhibitor by Docking Screening, Biochemical Assay, and in Vitro Studies. 2336-2343 - Scott A. Hollingsworth, Brian D. Nguyen, Georges Chreifi, Anton P. Arce, Thomas L. Poulos:
Insights into the Dynamics and Dissociation Mechanism of a Protein Redox Complex Using Molecular Dynamics. 2344-2350 - Yie-Vern Lee, Sy Bing Choi, Habibah A. Wahab, Yee-Siew Choong:
Active Site Flexibility of Mycobacterium tuberculosis Isocitrate Lyase in Dimer Form. 2351-2357 - Kun Song, Xinyi Liu, Wenkang Huang, Shaoyong Lu, Qiancheng Shen, Lu Zhang, Jian Zhang:
Improved Method for the Identification and Validation of Allosteric Sites. 2358-2363 - Pawel Krupa, Anna Halabis, Wioletta Zmudzinska, Stanislaw Oldziej, Harold A. Scheraga, Adam Liwo:
Maximum Likelihood Calibration of the UNRES Force Field for Simulation of Protein Structure and Dynamics. 2364-2377 - Prabir Khatua, Sudipta Kumar Sinha, Sanjoy Bandyopadhyay:
Size-Dependent Conformational Features of Aβ17-42 Protofilaments from Molecular Simulation Studies. 2378-2392 - Jagna Witek, Bettina G. Keller, Markus Blatter, Axel Meissner, Trixie Wagner, Sereina Riniker:
Correction to Kinetic Models of Cyclosporin A in Polar and Apolar Environments Reveal Multiple Congruent Conformational States. 2393
Volume 57, Number 10, October 2017
- Zhe Deng, Weizhong Tu, Zixin Deng, Qian-Nan Hu:
PhID: An Open-Access Integrated Pharmacology Interactions Database for Drugs, Targets, Diseases, Genes, Side-Effects, and Pathways. 2395-2400 - Reinis Danne, Chetan S. Poojari, Hector Martinez-Seara, Sami Rissanen, Fabio Lolicato, Tomasz Róg, Ilpo Vattulainen:
doGlycans-Tools for Preparing Carbohydrate Structures for Atomistic Simulations of Glycoproteins, Glycolipids, and Carbohydrate Polymers for GROMACS. 2401-2406 - Chen Jiang, Xi Jin:
Quick Way to Port Existing C/C++ Chemoinformatics Toolkits to the Web Using Emscripten. 2407-2412 - Baichuan Sun, Michael Fernández, Amanda S. Barnard:
Machine Learning for Silver Nanoparticle Electron Transfer Property Prediction. 2413-2423 - Iva Lukac, Joanna M. Zarnecka, Edward J. Griffen, Alexander G. Dossetter, Stephen A. St-Gallay, Steven J. Enoch, Judith C. Madden, Andrew G. Leach:
Turbocharging Matched Molecular Pair Analysis: Optimizing the Identification and Analysis of Pairs. 2424-2436 - Agnes Meyder, Eva Nittinger, Gudrun Lange, Robert Klein, Matthias Rarey:
Estimating Electron Density Support for Individual Atoms and Molecular Fragments in X-ray Structures. 2437-2447 - Nicolas Bosc, Mélaine A. Kuenemann, Jérôme Bécot, Marek Vavrusa, Adrien H. Cerdan, Olivier Sperandio:
Privileged Substructures to Modulate Protein-Protein Interactions. 2448-2462 - Pernille Sønderby, Åsmund Rinnan, Jesper J. Madsen, Pernille Harris, Jens T. Bukrinski, Günther H. J. Peters:
Small-Angle X-ray Scattering Data in Combination with RosettaDock Improves the Docking Energy Landscape. 2463-2475 - Meiting Wang, Pengfei Li, Xiangyu Jia, Wei Liu, Yihan Shao, Wenxin Hu, Jun Zheng, Bernard R. Brooks, Ye Mei:
Efficient Strategy for the Calculation of Solvation Free Energies in Water and Chloroform at the Quantum Mechanical/Molecular Mechanical Level. 2476-2489 - Yuting Xu, Junshui Ma, Andy Liaw, Robert P. Sheridan, Vladimir Svetnik:
Demystifying Multitask Deep Neural Networks for Quantitative Structure-Activity Relationships. 2490-2504 - Negin Forouzesh, Saeed Izadi, Alexey V. Onufriev:
Grid-Based Surface Generalized Born Model for Calculation of Electrostatic Binding Free Energies. 2505-2513 - Kai Liu, Hironori Kokubo:
Exploring the Stability of Ligand Binding Modes to Proteins by Molecular Dynamics Simulations: A Cross-docking Study. 2514-2522 - Kajwal Kumar Patra, Akash Bhattacharya, Swati Bhattacharya:
Allosteric Signal Transduction in HIV-1 Restriction Factor SAMHD1 Proceeds via Reciprocal Handshake across Monomers. 2523-2538 - Redona Izairi, Hiqmet Kamberaj:
Comparison Study of Polar and Nonpolar Contributions to Solvation Free Energy. 2539-2553 - Christopher Lockhart, Dmitri K. Klimov:
Cholesterol Changes the Mechanisms of Aβ Peptide Binding to the DMPC Bilayer. 2554-2565 - Patricia Gómez-Gutiérrez, Jaime Rubio-Martinez, Juan Jesús Pérez:
Identification of Potential Small Molecule Binding Pockets in p38α MAP Kinase. 2566-2574 - Lars Richter:
Topliss Batchwise Schemes Reviewed in the Era of Open Data Reveal Significant Differences between Enzymes and Membrane Receptors. 2575-2583 - Jean-Rémy Marchand, Andrea Dalle Vedove, Graziano Lolli, Amedeo Caflisch:
Discovery of Inhibitors of Four Bromodomains by Fragment-Anchored Ligand Docking. 2584-2597 - Julia R. Rogers, Seán McHugh, Yu-Shan Lin:
Predictions for α-Helical Glycopeptide Design from Structural Bioinformatics Analysis. 2598-2611
Volume 57, Number 11, November 2017
- Chloé Dequeker, Elodie Laine, Alessandra Carbone:
INTerface Builder: A Fast Protein-Protein Interface Reconstruction Tool. 2613-2617 - Pavel G. Polishchuk:
Interpretation of Quantitative Structure-Activity Relationship Models: Past, Present, and Future. 2618-2639 - Peter W. Kenny:
Comment on The Ecstasy and Agony of Assay Interference Compounds. 2640-2645 - Norio Yoshida:
Role of Solvation in Drug Design as Revealed by the Statistical Mechanics Integral Equation Theory of Liquids. 2646-2656 - Jiansong Fang, Zengrui Wu, Chuipu Cai, Qi Wang, Yun Tang, Feixiong Cheng:
Quantitative and Systems Pharmacology. 1. In Silico Prediction of Drug-Target Interactions of Natural Products Enables New Targeted Cancer Therapy. 2657-2671 - Youjun Xu, Jianfeng Pei, Luhua Lai:
Deep Learning Based Regression and Multiclass Models for Acute Oral Toxicity Prediction with Automatic Chemical Feature Extraction. 2672-2685 - Nanyi Wang, Lirong Wang, Xiang-Qun Xie:
ProSelection: A Novel Algorithm to Select Proper Protein Structure Subsets for in Silico Target Identification and Drug Discovery Research. 2686-2698 - Kyle V. Butler, Ian A. Macdonald, Nathaniel A. Hathaway, Jian Jin:
Report and Application of a Tool Compound Data Set. 2699-2706 - Ricardo Visini, Josep Arús-Pous, Mahendra Awale, Jean-Louis Reymond:
Virtual Exploration of the Ring Systems Chemical Universe. 2707-2718 - Nils-Ole Friedrich, Christina de Bruyn Kops, Florian Flachsenberg, Kai Sommer, Matthias Rarey, Johannes Kirchmair:
Benchmarking Commercial Conformer Ensemble Generators. 2719-2728 - P. G. Romano, Marina Guenza:
GRadient Adaptive Decomposition (GRAD) Method: Optimized Refinement Along Macrostate Borders in Markov State Models. 2729-2740 - Stephanie K. Ashenden, Thierry Kogej, Ola Engkvist, Andreas Bender:
Innovation in Small-Molecule-Druggable Chemical Space: Where are the Initial Modulators of New Targets Published? 2741-2753 - Ruth I. J. Amos, Eva Tyteca, Mohammad Talebi, Paul R. Haddad, Roman Szucs, John W. Dolan, Christopher A. Pohl:
Benchmarking of Computational Methods for Creation of Retention Models in Quantitative Structure-Retention Relationships Studies. 2754-2762 - Haiyang Zhang, Yang Jiang, Hai Yan, Ziheng Cui, Chunhua Yin:
Comparative Assessment of Computational Methods for Free Energy Calculations of Ionic Hydration. 2763-2775 - Irene Luque Ruiz, Miguel Ángel Gómez-Nieto:
Advantages of Relative versus Absolute Data for the Development of Quantitative Structure-Activity Relationship Classification Models. 2776-2788 - Takeshi Hasegawa, Masatake Sugita, Takeshi Kikuchi, Fumio Hirata:
A Systematic Analysis of the Binding Affinity between the Pim-1 Kinase and Its Inhibitors Based on the MM/3D-RISM/KH Method. 2789-2798 - Anastasia G. Konshina, Nikolay A. Krylov, Roman G. Efremov:
Cardiotoxins: Functional Role of Local Conformational Changes. 2799-2810 - Shuang Hou, Ruo-Xu Gu, Dong-Qing Wei:
Inhibition of β-Amyloid Channels with a Drug Candidate wgx-50 Revealed by Molecular Dynamics Simulations. 2811-2821 - Christian A. Hanke, Holger Gohlke:
Tertiary Interactions in the Unbound Guanine-Sensing Riboswitch Focus Functional Conformational Variability on the Binding Site. 2822-2832 - Themis Lazaridis, Gerhard Hummer:
Classical Molecular Dynamics with Mobile Protons. 2833-2845 - Babitha Machireddy, Gurmannat Kalra, Subash Jonnalagadda, Kandalam Ramanujachary, Chun Wu:
Probing the Binding Pathway of BRACO19 to a Parallel-Stranded Human Telomeric G-Quadruplex Using Molecular Dynamics Binding Simulation with AMBER DNA OL15 and Ligand GAFF2 Force Fields. 2846-2864 - Francesco Manzoni, Jon Uranga, Samuel Genheden, Ulf Ryde:
Can System Truncation Speed up Ligand-Binding Calculations with Periodic Free-Energy Simulations? 2865-2873 - Daniela Trisciuzzi, Domenico Alberga, Kamel Mansouri, Richard S. Judson, Ettore Novellino, Giuseppe Felice Mangiatordi, Orazio Nicolotti:
Predictive Structure-Based Toxicology Approaches To Assess the Androgenic Potential of Chemicals. 2874-2884 - Jade Fogha, Bogdan Marekha, Marcella De Giorgi, Anne Sophie Voisin-Chiret, Sylvain Rault, Ronan Bureau, Jana Sopkova-de Oliveira Santos:
Toward Understanding Mcl-1 Promiscuous and Specific Binding Mode. 2885-2895 - Lina Wang, Shao-Ping Shi, Ping-Ping Wen, Zhi-You Zhou, Jian-Ding Qiu:
Computing Prediction and Functional Analysis of Prokaryotic Propionylation. 2896-2904
Volume 57, Number 12, December 2017
- Antonella Zanzi, Clemens Wittwehr:
Searching Online Chemical Data Repositories via the ChemAgora Portal. 2905-2910 - Zoe Cournia, Bryce K. Allen, Woody Sherman:
Relative Binding Free Energy Calculations in Drug Discovery: Recent Advances and Practical Considerations. 2911-2937 - Tomohiro Sato, Noriaki Hashimoto, Teruki Honma:
Bioisostere Identification by Determining the Amino Acid Binding Preferences of Common Chemical Fragments. 2938-2947 - Xiao Li, Yuan Zhang, Hongna Chen, Huanhuan Li, Yong Zhao:
Insights into the Molecular Basis of the Acute Contact Toxicity of Diverse Organic Chemicals in the Honey Bee. 2948-2957 - Junfeng Liu, Xia Ning:
Differential Compound Prioritization via Bidirectional Selectivity Push with Power. 2958-2975 - Gary Tresadern, Andrés A. Trabanco, Laura Pérez-Benito, John P. Overington, Herman W. T. van Vlijmen, Gerard J. P. van Westen:
Identification of Allosteric Modulators of Metabotropic Glutamate 7 Receptor Using Proteochemometric Modeling. 2976-2985 - Valentin Goussard, François Duprat, Vincent Gerbaud, Jean-Luc Ploix, Gérard Dreyfus, Véronique Nardello-Rataj, Jean-Marie Aubry:
Predicting the Surface Tension of Liquids: Comparison of Four Modeling Approaches and Application to Cosmetic Oils. 2986-2995 - Chiduru Watanabe, Hirofumi Watanabe, Kaori Fukuzawa, Lorien J. Parker, Yoshio Okiyama, Hitomi Yuki, Shigeyuki Yokoyama, Hirofumi Nakano, Shigenori Tanaka, Teruki Honma:
Theoretical Analysis of Activity Cliffs among Benzofuranone-Class Pim1 Inhibitors Using the Fragment Molecular Orbital Method with Molecular Mechanics Poisson-Boltzmann Surface Area (FMO+MM-PBSA) Approach. 2996-3010 - Hubert Li, Manbir Sandhu, Linda H. Malkas, Robert J. Hickey, Nagarajan Vaidehi:
How Does the Proliferating Cell Nuclear Antigen Modulate Binding Specificity to Multiple Partner Proteins? 3011-3021 - Waleed A. Zalloum, Hiba M. Zalloum:
Exploring the Active Center of the LSD1/CoREST Complex by Molecular Dynamics Simulation Utilizing Its Co-crystallized Co-factor Tetrahydrofolate as a Probe. 3022-3031 - Bercem Dutagaci, Michael Feig:
Determination of Hydrophobic Lengths of Membrane Proteins with the HDGB Implicit Membrane Model. 3032-3042 - Ariela Vergara Jaque, Peying Fong, Jeffrey Comer:
Iodide Binding in Sodium-Coupled Cotransporters. 3043-3055 - Melanie L. Aprahamian, Svetlana B. Tikunova, Morgan V. Price, Andres F. Cuesta, Jonathan P. Davis, Steffen Lindert:
Successful Identification of Cardiac Troponin Calcium Sensitizers Using a Combination of Virtual Screening and ROC Analysis of Known Troponin C Binders. 3056-3069 - Ryuhei Harada, Yasuteru Shigeta:
Self-Avoiding Conformational Sampling Based on Histories of Past Conformational Searches. 3070-3078 - Samo Turk, Benjamin Merget, Friedrich Rippmann, Simone Fulle:
Coupling Matched Molecular Pairs with Machine Learning for Virtual Compound Optimization. 3079-3085 - Charles H. Reynolds, Ryan C. Reynolds:
Group Additivity in Ligand Binding Affinity: An Alternative Approach to Ligand Efficiency. 3086-3093 - Marko Jukic, Janez Konc, Stanislav Gobec, Dusanka Janezic:
Identification of Conserved Water Sites in Protein Structures for Drug Design. 3094-3103 - Antonella Ciancetta, Robert D. O'Connor, Silvia Paoletta, Kenneth A. Jacobson:
Demystifying P2Y1 Receptor Ligand Recognition through Docking and Molecular Dynamics Analyses. 3104-3123 - Richard Lonsdale, Jonathan Burgess, Nicola Colclough, Nichola L. Davies, Eva M. Lenz, Alexandra L. Orton, Richard A. Ward:
Expanding the Armory: Predicting and Tuning Covalent Warhead Reactivity. 3124-3137 - Yeu-Chern Harn, Bo-Han Su, Yuan-Ling Ku, Olivia A. Lin, Cheng-Fu Chou, Yufeng J. Tseng:
NP-StructurePredictor: Prediction of Unknown Natural Products in Plant Mixtures. 3138-3148 - Yijie Ding, Jijun Tang, Fei Guo:
Identification of Protein-Ligand Binding Sites by Sequence Information and Ensemble Classifier. 3149-3161 - Luca Belmonte, Sheref S. Mansy:
Patterns of Ligands Coordinated to Metallocofactors Extracted from the Protein Data Bank. 3162-3171
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