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ORCIDJournal of Chemical Information and Modeling, Volume 58
Volume 58, Number 1, January 2018
- Daniel Probst
, Jean-Louis Reymond:
SmilesDrawer: Parsing and Drawing SMILES-Encoded Molecular Structures Using Client-Side JavaScript. 1-7 - Sergey Ivanov, Alexey Lagunin, Anastasia V. Rudik, Dmitry Filimonov, Vladimir Poroikov:
ADVERPred-Web Service for Prediction of Adverse Effects of Drugs. 8-11 - Didier Mathieu:
Atom Pair Contribution Method: Fast and General Procedure To Predict Molecular Formation Enthalpies. 12-26 - Sabrina Jaeger, Simone Fulle, Samo Turk:
Mol2vec: Unsupervised Machine Learning Approach with Chemical Intuition. 27-35 - Yue Kong, Andreas Bender, Aixia Yan:
Identification of Novel Aurora Kinase A (AURKA) Inhibitors via Hierarchical Ligand-Based Virtual Screening. 36-47 - Ondrej Gutten, Daniel Bím, Jan Rezác, Lubomír Rulísek:
Macrocycle Conformational Sampling by DFT-D3/COSMO-RS Methodology. 48-60 - Suzanne McAnanama-Brereton, Mark P. Waller:
Rational Density Functional Selection Using Game Theory. 61-67 - Devawati Dutta, Ranjita Das, Chhabinath Mandal, Chitra Mandal:
Structure-Based Kinase Profiling To Understand the Polypharmacological Behavior of Therapeutic Molecules. 68-89 - Antoine Marion, Jerzy Góra, Oliver Kracker, Tanja Fröhr, Rafal Latajka, Norbert Sewald, Iris Antes:
Amber-Compatible Parametrization Procedure for Peptide-like Compounds: Application to 1, 4- and 1, 5-Substituted Triazole-Based Peptidomimetics. 90-110 - Mark A. Olson:
Parallel Tempering of Dark Matter from the Ebola Virus Proteome: Comparison of CHARMM36m and CHARMM22 Force Fields with Implicit Solvent. 111-118 - Hossam M. Ashtawy, Nihar R. Mahapatra:
Task-Specific Scoring Functions for Predicting Ligand Binding Poses and Affinity and for Screening Enrichment. 119-133 - Hossam M. Ashtawy, Nihar R. Mahapatra:
Descriptor Data Bank (DDB): A Cloud Platform for Multiperspective Modeling of Protein-Ligand Interactions. 134-147 - John J. Irwin, Garrett Gaskins, Teague Sterling, Michael M. Mysinger, Michael J. Keiser:
Predicted Biological Activity of Purchasable Chemical Space. 148-164 - Jan Dreher, Josef Scheiber, Nikolaus Stiefl, Knut Baumann:
xMaP - An Interpretable Alignment-Free Four-Dimensional Quantitative Structure-Activity Relationship Technique Based on Molecular Surface Properties and Conformer Ensembles. 165-181 - Kh. Dhanachandra Singh, Hamiyet Unal, Russell Desnoyer, Sadashiva S. Karnik:
Divergent Spatiotemporal Interaction of Angiotensin Receptor Blocking Drugs with Angiotensin Type 1 Receptor. 182-193 - Zhaomin Liu, Stephen J. Barigye, Moeed Shahamat, Paul Labute, Nicolas Moitessier:
Atom Types Independent Molecular Mechanics Method for Predicting the Conformational Energy of Small Molecules. 194-205 - Pawel Krupa, Anna Halabis, Wioletta Zmudzinska, Stanislaw Oldziej, Harold A. Scheraga, Adam Liwo:
Correction to Maximum Likelihood Calibration of the UNRES Force Field for Simulation of Protein Structure and Dynamics. 206
Volume 58, Number 2, February 2018
- Gregor Urban, Niranjan Subrahmanya, Pierre Baldi:
Inner and Outer Recursive Neural Networks for Chemoinformatics Applications. 207-211 - Stephen J. Capuzzi, Thomas E. Thornton, Kammy Liu, Nancy Baker, Wai In Lam, Colin P. O'banion, Eugene N. Muratov, Diane Pozefsky, Alexander Tropsha:
Chemotext: A Publicly Available Web Server for Mining Drug-Target-Disease Relationships in PubMed. 212-218 - Sergio Decherchi, Giovanni Bottegoni, Andrea Spitaleri, Walter Rocchia, Andrea Cavalli:
BiKi Life Sciences: A New Suite for Molecular Dynamics and Related Methods in Drug Discovery. 219-224 - Darwin Y. Fu, Jens Meiler:
Predictive Power of Different Types of Experimental Restraints in Small Molecule Docking: A Review. 225-233 - Mark H. Barley, Nicholas J. Turner, Royston Goodacre:
Improved Descriptors for the Quantitative Structure-Activity Relationship Modeling of Peptides and Proteins. 234-243 - Sanghoon Park, Baekjun Kim, Sihoon Choi, Peter G. Boyd, Berend Smit, Jihan Kim:
Text Mining Metal-Organic Framework Papers. 244-251 - Connor W. Coley, Luke Rogers, William H. Green Jr., Klavs F. Jensen:
SCScore: Synthetic Complexity Learned from a Reaction Corpus. 252-261 - Ali Bakiri, Jane Hubert, Romain Reynaud, Carole Lambert, Agathe Martinez, Jean-Hugues Renault, Jean-Marc Nuzillard:
Reconstruction of HMBC Correlation Networks: A Novel NMR-Based Contribution to Metabolite Mixture Analysis. 262-270 - Haoyu S. Yu, Mark A. Watson, Art D. Bochevarov:
Weighted Averaging Scheme and Local Atomic Descriptor for pKa Prediction Based on Density Functional Theory. 271-286 - José Jiménez, Miha Skalic, Gerard Martínez-Rosell, Gianni De Fabritiis:
KDEEP: Protein-Ligand Absolute Binding Affinity Prediction via 3D-Convolutional Neural Networks. 287-296 - Ventsislav Yordanov, Ivan Dimitrov, Irini A. Doytchinova:
Proteochemometrics-Based Prediction of Peptide Binding to HLA-DP Proteins. 297-304 - Sarah E. Graham, Richard D. Smith, Heather A. Carlson:
Predicting Displaceable Water Sites Using Mixed-Solvent Molecular Dynamics. 305-314 - Jean-Noël Grad, Alba Gigante, Christoph Wilms, Jan Nikolaj Dybowski, Ludwig Ohl, Christian Ottmann, Carsten Schmuck, Daniel Hoffmann:
Locating Large, Flexible Ligands on Proteins. 315-327 - Soumya Lipsa Rath, Huihui Liu, Susumu Okazaki, Wataru Shinoda:
Identification of Factors Promoting HBV Capsid Self-Assembly by Assembly-Promoting Antivirals. 328-337 - Andrew Yeager, Kathryn Humphries, Ellen Farmer, Gene Cline, Bill R. Miller:
Investigation of Nascent Base Pair and Polymerase Behavior in the Presence of Mismatches in DNA Polymerase I Using Molecular Dynamics. 338-349 - Axel Rudling, Adolfo Orro, Jens Carlsson:
Prediction of Ordered Water Molecules in Protein Binding Sites from Molecular Dynamics Simulations: The Impact of Ligand Binding on Hydration Networks. 350-361 - Samira Hezaveh, An-Ping Zeng, Uwe Jandt:
Full Enzyme Complex Simulation: Interactions in Human Pyruvate Dehydrogenase Complex. 362-369 - Souvik Sinha, Atanu Maity, Shubhra Ghosh Dastidar:
BIM Binding Remotely Regulates BAX Activation: Insights from the Free Energy Landscapes. 370-382 - David L. Penkler, Canan Atilgan, Özlem Tastan Bishop:
Allosteric Modulation of Human Hsp90α Conformational Dynamics. 383-404 - Gabrielle Stetz, Gennady M. Verkhivker:
Functional Role and Hierarchy of the Intermolecular Interactions in Binding of Protein Kinase Clients to the Hsp90-Cdc37 Chaperone: Structure-Based Network Modeling of Allosteric Regulation. 405-421 - Yufei Yue, Yue Ma, Ping Qian, Hong Guo:
Catalytic Mechanism of the Ubiquitin-Like NEDD8 Transfer in RING E3-E2∼NEDD8-Target Complex from QM/MM Free Energy Simulations. 422-429 - Huanyu Chu, Haiyan Liu:
TetraBASE: A Side Chain-Independent Statistical Energy for Designing Realistically Packed Protein Backbones. 430-442 - José D. Colbes, Sergio A. Aguila, Carlos A. Brizuela:
Scoring of Side-Chain Packings: An Analysis of Weight Factors and Molecular Dynamics Structures. 443-452 - Swati R. Manjari, Nilesh K. Banavali:
Structural Articulation of Biochemical Reactions Using Restrained Geometries and Topology Switching. 453-463 - Chimno I. Nnadi, Meredith L. Jenkins, Daniel R. Gentile, Leslie A. Bateman, Daniel Zaidman, Trent E. Balius, Daniel K. Nomura, John E. Burke, Kevan M. Shokat, Nir London:
Novel K-Ras G12C Switch-II Covalent Binders Destabilize Ras and Accelerate Nucleotide Exchange. 464-471 - Alex T. Müller, Jan A. Hiss, Gisbert Schneider:
Recurrent Neural Network Model for Constructive Peptide Design. 472-479 - Hiromasa Kaneko:
Discussion on Regression Methods Based on Ensemble Learning and Applicability Domains of Linear Submodels. 480-489 - Martina Bertazzo, Mattia Bernetti, Maurizio Recanatini, Matteo Masetti, Andrea Cavalli:
Fully Flexible Docking via Reaction-Coordinate-Independent Molecular Dynamics Simulations. 490-500 - Jun Hu, Yang Li, Yang Zhang, Dong-Jun Yu:
ATPbind: Accurate Protein-ATP Binding Site Prediction by Combining Sequence-Profiling and Structure-Based Comparisons. 501-510 - Ari Hardianto, Fei Liu, Shoba Ranganathan:
Molecular Dynamics Pinpoint the Global Fluorine Effect in Balanoid Binding to PKCε and PKA. 511-519 - Kedi Wu, Guo-Wei Wei:
Quantitative Toxicity Prediction Using Topology Based Multitask Deep Neural Networks. 520-531 - Jiawen Chen, Bo Wang, Yinghao Wu:
Structural Characterization and Function Prediction of Immunoglobulin-like Fold in Cell Adhesion and Cell Signaling. 532-542
Volume 58, Number 3, March 2018
- Dimitra-Danai Varsou, Georgia Tsiliki, Penny Nymark, Pekka Kohonen, Roland Grafstrom, Haralambos Sarimveis:
toxFlow: A Web-Based Application for Read-Across Toxicity Prediction Using Omics and Physicochemical Data. 543-549 - Zhihong Liu, Jiewen Du, Xin Yan, Jiali Zhong, Lu Cui, Jinyuan Lin, Lizhu Zeng, Peng Ding, Pin Chen, Xinxin Zhou, Huihao Zhou, Qiong Gu, Jun Xu:
TCMAnalyzer: A Chemo- and Bioinformatics Web Service for Analyzing Traditional Chinese Medicine. 550-555 - Haohao Fu, James C. Gumbart, Haochuan Chen, Xueguang Shao, Wensheng Cai, Christophe Chipot:
BFEE: A User-Friendly Graphical Interface Facilitating Absolute Binding Free-Energy Calculations. 556-560 - Jaime Rodríguez-Guerra Pedregal, Pablo Gómez-Orellana, Jean-Didier Maréchal:
ESIgen: Electronic Supporting Information Generator for Computational Chemistry Publications. 561-564 - Sereina Riniker:
Fixed-Charge Atomistic Force Fields for Molecular Dynamics Simulations in the Condensed Phase: An Overview. 565-578 - Patrick Bleiziffer, Kay Schaller, Sereina Riniker:
Machine Learning of Partial Charges Derived from High-Quality Quantum-Mechanical Calculations. 579-590 - L. Mark Hall, Dennis W. Hill, Kelly Bugden, Shannon Cawley, Lowell H. Hall, Ming-Hui Chen, David F. Grant:
Development of a Reverse Phase HPLC Retention Index Model for Nontargeted Metabolomics Using Synthetic Compounds. 591-604 - Spandana Makeneni, David F. Thieker, Robert J. Woods:
Applying Pose Clustering and MD Simulations To Eliminate False Positives in Molecular Docking. 605-614 - Jason C. Cole, Oliver Korb, Patrick McCabe, Murray G. Read, Robin Taylor:
Knowledge-Based Conformer Generation Using the Cambridge Structural Database. 615-629 - Julian Zaugg, Yosephine Gumulya, Mikael Bodén, Alan E. Mark, Alpeshkumar K. Malde:
Effect of Binding on Enantioselectivity of Epoxide Hydrolase. 630-640 - Álvaro Cortés Cabrera, Paula M. Petrone:
Optimal HTS Fingerprint Definitions by Using a Desirability Function and a Genetic Algorithm. 641-646 - Kartheek Pitta, Marimuthu Krishnan:
Molecular Mechanism, Dynamics, and Energetics of Protein-Mediated Dinucleotide Flipping in a Mismatched DNA: A Computational Study of the RAD4-DNA Complex. 647-660 - Emel Timuçin, Osman Ugur Sezerman:
Thermostability of the PYL-PP2C Heterodimer Is Dependent on Magnesium: In Silico Insights into the Link between Heat Stress Response and Magnesium Deficiency in Plants. 661-672 - Mukesh Patel, Martyn L. Chilton, Andrea Sartini, Laura Gibson, Chris Barber, Liz Covey-Crump, Katarzyna R. Przybylak, Mark T. D. Cronin, Judith C. Madden:
Assessment and Reproducibility of Quantitative Structure-Activity Relationship Models by the Nonexpert. 673-682 - Gerard Martínez-Rosell, Matt J. Harvey, Gianni De Fabritiis:
Molecular-Simulation-Driven Fragment Screening for the Discovery of New CXCL12 Inhibitors. 683-691 - Denis Bucher, Pieter F. W. Stouten, Nicolas Triballeau:
Shedding Light on Important Waters for Drug Design: Simulations versus Grid-Based Methods. 692-699 - Hwangseo Park, Hoi-Yun Jung, Shinmee Mah, Sungwoo Hong:
Systematic Computational Design and Identification of Low Picomolar Inhibitors of Aurora Kinase A. 700-709 - Joana Magalhães, Giannamaria Annunziato, Nina Franko, Marco Pieroni, Barbara Campanini, Agostino Bruno, Gabriele Costantino:
Integration of Enhanced Sampling Methods with Saturation Transfer Difference Experiments to Identify Protein Druggable Pockets. 710-723 - Xinxiang Wang, Di Zhang, Sheng-You Huang:
New Knowledge-Based Scoring Function with Inclusion of Backbone Conformational Entropies from Protein Structures. 724-732 - Hamid Hadi-Alijanvand, Maryam Rouhani:
Partner-Specific Prediction of Protein-Dimer Stability from Unbound Structure of Monomer. 733-745
Volume 58, Number 4, April 2018
- Songling Ma, Sungbo Hwang, Se-Han Lee, William E. Acree Jr., Kyoung Tai No:
Incorporation of Hydrogen Bond Angle Dependency into the Generalized Solvation Free Energy Density Model. 761-772 - Yossa Dwi Hartono, You Xu, Andrey Karshikoff, Lennart Nilsson, Alessandra Villa:
Modeling pK Shift in DNA Triplexes Containing Locked Nucleic Acids. 773-783 - Phani Ghanakota, Herman van Vlijmen, Woody Sherman, Thijs Beuming:
Large-Scale Validation of Mixed-Solvent Simulations to Assess Hotspots at Protein-Protein Interaction Interfaces. 784-793 - Panagiotis Lagarias, Eleni Vrontaki, George Lambrinidis, Dimitrios Stamatis, Marino Convertino, Gabriella Ortore, Thomas M. Mavromoustakos, Karl Norbert Klotz, Antonios Kolocouris:
Discovery of Novel Adenosine Receptor Antagonists through a Combined Structure- and Ligand-Based Approach Followed by Molecular Dynamics Investigation of Ligand Binding Mode. 794-815 - Xiaozheng Zhang, Fengchao Cui, Hongqian Chen, Tianshu Zhang, Kecheng Yang, Yibo Wang, Zhenyan Jiang, Kenner C. Rice, Linda R. Watkins, Mark R. Hutchinson, Yunqi Li, Yinghua Peng, Xiaohui Wang:
Dissecting the Innate Immune Recognition of Opioid Inactive Isomer (+)-Naltrexone Derived Toll-like Receptor 4 (TLR4) Antagonists. 816-825 - Ramin Ekhteiari Salmas, Philip Seeman, Matthias Stein, Serdar Durdagi:
Structural Investigation of the Dopamine-2 Receptor Agonist Bromocriptine Binding to Dimeric D2HighR and D2LowR States. 826-836 - Xi Chen, Qiang Gan, Changgen Feng, Xia Liu, Qian Zhang:
Virtual Screening of Novel and Selective Inhibitors of Protein Tyrosine Phosphatase 1B over T-Cell Protein Tyrosine Phosphatase Using a Bidentate Inhibition Strategy. 837-847 - Dusan Petrovic, Ansgar Bokel, Matthew Allan, Vlada B. Urlacher, Birgit Strodel:
Simulation-Guided Design of Cytochrome P450 for Chemo- and Regioselective Macrocyclic Oxidation. 848-858 - Tifang Miao, Qinghua Deng, Hui Gao, Xianliang Fu, Shuang Li:
Theoretical Studies on DNA-Cleavage Mechanism of Copper(II) Complexes: Probing Generation of Reactive Oxygen Species. 859-866 - Lucía Romero, Jordi Cano, Julio Gomis-Tena, Beatriz Trénor, Ferran Sanz, Manuel Pastor, Javier Saiz:
In Silico QT and APD Prolongation Assay for Early Screening of Drug-Induced Proarrhythmic Risk. 867-878 - Mámon M. Hatmal, Mutasem O. Taha:
Combining Stochastic Deformation/Relaxation and Intermolecular Contacts Analysis for Extracting Pharmacophores from Ligand-Receptor Complexes. 879-893
Volume 58, Number 5, May 2018
- Sharon L. Guffy, Frank D. Teets, Minnie I. Langlois, Brian Kuhlman:
Protocols for Requirement-Driven Protein Design in the Rosetta Modeling Program. 895-901 - Andrew Dalke, Jérôme Hert, Christian Kramer:
mmpdb: An Open-Source Matched Molecular Pair Platform for Large Multiproperty Data Sets. 902-910 - M. Katharine Holloway, Georgia B. McGaughey:
Computational Chemistry: A Rising Tide of Women. 911-915 - Izhar Wallach, Abraham Heifets:
Most Ligand-Based Classification Benchmarks Reward Memorization Rather than Generalization. 916-932 - Dipan Ghosh, Uwe Koch, Kamyar Hadian, Michael Sattler, Igor V. Tetko:
Luciferase Advisor: High-Accuracy Model To Flag False Positive Hits in Luciferase HTS Assays. 933-942 - Chuipu Cai, Jiansong Fang, Pengfei Guo, Qi Wang, Huixiao Hong, Javid Moslehi, Feixiong Cheng:
In Silico Pharmacoepidemiologic Evaluation of Drug-Induced Cardiovascular Complications Using Combined Classifiers. 943-956 - Sorin I. Avram, Alina Bora, Liliana Halip, Ramona Curpan:
Modeling Kinase Inhibition Using Highly Confident Data Sets. 957-967 - Wanli You, Chia-en A. Chang:
Role of Molecular Interactions and Protein Rearrangement in the Dissociation Kinetics of p38α MAP Kinase Type-I/II/III Inhibitors. 968-981 - Anna S. Kamenik, Uta F. Lessel, Julian E. Fuchs, Thomas Fox, Klaus R. Liedl:
Peptidic Macrocycles - Conformational Sampling and Thermodynamic Characterization. 982-992 - Fang-Yu Lin, Pedro E. M. Lopes, Edward Harder, Benoît Roux, Alexander D. MacKerell Jr.:
Polarizable Force Field for Molecular Ions Based on the Classical Drude Oscillator. 993-1004 - Anna Theresa Cavasin, Alexander Hillisch, Felix Uellendahl, Sebastian Schneckener, Andreas H. Göller:
Reliable and Performant Identification of Low-Energy Conformers in the Gas Phase and Water. 1005-1020 - Steven A. Combs, Benjamin K. Mueller, Jens Meiler:
Holistic Approach to Partial Covalent Interactions in Protein Structure Prediction and Design with Rosetta. 1021-1036 - Haiyang Zhang, Chunhua Yin, Yang Jiang, David van der Spoel:
Force Field Benchmark of Amino Acids: I. Hydration and Diffusion in Different Water Models. 1037-1052 - Amy K. Smith, Dmitri K. Klimov:
Binding of Cytotoxic Aβ25-35 Peptide to the Dimyristoylphosphatidylcholine Lipid Bilayer. 1053-1065 - Fei Ye, Weiyao Zhang, Xiaoqing Ye, Jia Jin, Zhengbing Lv, Cheng Luo:
Identification of Selective, Cell Active Inhibitors of Protein Arginine Methyltransferase 5 through Structure-Based Virtual Screening and Biological Assays. 1066-1073 - Mireia Jiménez-Rosés, Minos-Timotheos Matsoukas, Gianluigi Caltabiano, Arnau Cordomí:
Ligand-Triggered Structural Changes in the M2 Muscarinic Acetylcholine Receptor. 1074-1082 - Ekaterina A. Sosnina, Dmitry I. Osolodkin, Eugene V. Radchenko, Sergey B. Sosnin, Vladimir A. Palyulin:
Influence of Descriptor Implementation on Compound Ranking Based on Multiparameter Assessment. 1083-1093 - Noé Sturm, Annachiara Tinivella, Giulio Rastelli:
Exploration and Comparison of the Geometrical and Physicochemical Properties of an αC Allosteric Pocket in the Structural Kinome. 1094-1103 - Jie Xia, Terry-Elinor Reid, Song Wu, Liangren Zhang, Xiang Simon Wang:
Maximal Unbiased Benchmarking Data Sets for Human Chemokine Receptors and Comparative Analysis. 1104-1120 - Claas Strecker, Bernd Meyer:
Plasticity of the Binding Site of Renin: Optimized Selection of Protein Structures for Ensemble Docking. 1121-1131 - Fredrik Svensson, Natália Aniceto, Ulf Norinder, Isidro Cortes-Ciriano, Ola Spjuth, Lars Carlsson, Andreas Bender:
Conformal Regression for Quantitative Structure-Activity Relationship Modeling - Quantifying Prediction Uncertainty. 1132-1140 - Boris Vishnepolsky, Andrei E. Gabrielian, Alex Rosenthal, Darrell E. Hurt, Michael Tartakovsky, Grigol Managadze, Maya Grigolava, George I. Makhatadze, Malak Pirtskhalava:
Predictive Model of Linear Antimicrobial Peptides Active against Gram-Negative Bacteria. 1141-1151
Volume 58, Number 6, June 2018
- Kenneth M. Merz Jr.:
Investing in the Future. 1153 - Alessandro Pedretti, Angelica Mazzolari, Giulio Vistoli:
WarpEngine, a Flexible Platform for Distributed Computing Implemented in the VEGA Program and Specially Targeted for Virtual Screening Studies. 1154-1160 - Kira A. Armacost:
The Transition from Academia: Overcoming the Barrier to a Career in the Drug Discovery Industry. 1161-1163 - Myungshim Kang, Kaushik Chakraborty, Sharon M. Loverde:
Molecular Dynamics Simulations of Supramolecular Anticancer Nanotubes. 1164-1168 - Yingchun Cai, Hongbin Yang, Weihua Li, Guixia Liu, Philip W. Lee, Yun Tang:
Multiclassification Prediction of Enzymatic Reactions for Oxidoreductases and Hydrolases Using Reaction Fingerprints and Machine Learning Methods. 1169-1181 - Jun Shang, Ben Hu, Junmei Wang, Feng Zhu, Yu Kang, Dan Li, Huiyong Sun, De-Xin Kong, Tingjun Hou:
Cheminformatic Insight into the Differences between Terrestrial and Marine Originated Natural Products. 1182-1193 - Evgeny Putin, Arip Asadulaev, Yan Ivanenkov, Vladimir Aladinskiy, Benjamín Sánchez-Lengeling, Alán Aspuru-Guzik, Alex Zhavoronkov:
Reinforced Adversarial Neural Computer for de Novo Molecular Design. 1194-1204 - Elton José Ferreira Chaves, Itácio Q. M. Padilha, Demétrius A. M. Araújo, Gerd Bruno Rocha:
Determining the Relative Binding Affinity of Ricin Toxin A Inhibitors by Using Molecular Docking and Nonequilibrium Work. 1205-1213 - Vinicius M. Alves, Alexander Golbraikh, Stephen J. Capuzzi, Kammy Liu, Wai In Lam, Daniel Robert Korn, Diane Pozefsky, Carolina Horta Andrade, Eugene N. Muratov, Alexander Tropsha:
Multi-Descriptor Read Across (MuDRA): A Simple and Transparent Approach for Developing Accurate Quantitative Structure-Activity Relationship Models. 1214-1223 - Vishal B. Siramshetty, Qiaofeng Chen, Prashanth Devarakonda, Robert Preissner:
The Catch-22 of Predicting hERG Blockade Using Publicly Accessible Bioactivity Data. 1224-1233 - Jonghun Won, Gyu Rie Lee, Hahnbeom Park, Chaok Seok:
GalaxyGPCRloop: Template-Based and Ab Initio Structure Sampling of the Extracellular Loops of G-Protein-Coupled Receptors. 1234-1243 - Ara M. Abramyan, Matthias Quick, Catherine Xue, Jonathan A. Javitch, Lei Shi:
Exploring Substrate Binding in the Extracellular Vestibule of MhsT by Atomistic Simulations and Markov Models. 1244-1252 - Samiul M. Ansari, David S. Palmer:
Comparative Molecular Field Analysis Using Molecular Integral Equation Theory. 1253-1265 - Timothy E. H. Allen, Matthew N. Grayson, Jonathan M. Goodman, Steve Gutsell, Paul J. Russell:
Using Transition State Modeling To Predict Mutagenicity for Michael Acceptors. 1266-1271 - Man Cao, Guodong Chen, Lina Wang, Pingping Wen, Shaoping Shi:
Computational Prediction and Analysis for Tyrosine Post-Translational Modifications via Elastic Net. 1272-1281 - Siyang Tian, Yannick Djoumbou Feunang, Russell Greiner, David S. Wishart:
CypReact: A Software Tool for in Silico Reactant Prediction for Human Cytochrome P450 Enzymes. 1282-1291 - Pei Zhou, Botong Li, Yumeng Yan, Bowen Jin, Libang Wang, Sheng-You Huang:
Hierarchical Flexible Peptide Docking by Conformer Generation and Ensemble Docking of Peptides. 1292-1302 - Yu-Jiao Yang, Shuai Wang, Biao Zhang, Hong-Bin Shen:
Resolution Measurement from a Single Reconstructed Cryo-EM Density Map with Multiscale Spectral Analysis. 1303-1311 - Juan Pablo Arcon, Lucas A. Defelipe, Carlos P. Modenutti, Elias D. López, Daniel Alvarez-Garcia, Xavier Barril, Adrian Gustavo Turjanski, Marcelo A. Marti:
Correction to Molecular Dynamics in Mixed Solvents Reveals Protein-Ligand Interactions, Improves Docking and Allows Accurate Binding Free Energy Predictions. 1312
Volume 58, Number 7, July 2018
- Hanoch Senderowitz, Alexander Tropsha:
Materials Informatics. 1313-1314 - Haochuan Chen, Haohao Fu, Xueguang Shao, Christophe Chipot, Wensheng Cai:
ELF: An Extended-Lagrangian Free Energy Calculation Module for Multiple Molecular Dynamics Engines. 1315-1318 - Federico Fogolari, Ornela Maloku, Cedrix Jurgal Dongmo Foumthuim, Alessandra Corazza, Gennaro Esposito:
PDB2ENTROPY and PDB2TRENT: Conformational and Translational-Rotational Entropy from Molecular Ensembles. 1319-1324 - Xin-Qiu Yao, Mohamed Momin, Donald Hamelberg:
Elucidating Allosteric Communications in Proteins with Difference Contact Network Analysis. 1325-1330 - Pablo H. Palestro, Nicolas Enrique, Sofia Goicoechea, María L. Villalba, Laureano L. Sabatier, Pedro Martín, Verónica Milesi, Luis Bruno Blanch, Luciana Gavernet:
Searching for New Leads To Treat Epilepsy: Target-Based Virtual Screening for the Discovery of Anticonvulsant Agents. 1331-1342 - Malte Döntgen, Felix Schmalz, Wassja A. Kopp, Leif C. Kröger, Kai Leonhard:
Automated Chemical Kinetic Modeling via Hybrid Reactive Molecular Dynamics and Quantum Chemistry Simulations. 1343-1355 - Junchao Xia, William F. Flynn, Ronald M. Levy:
Improving Prediction Accuracy of Binding Free Energies and Poses of HIV Integrase Complexes Using the Binding Energy Distribution Analysis Method with Flattening Potentials. 1356-1371 - Yandong Huang, Robert C. Harris, Jana Shen:
Generalized Born Based Continuous Constant pH Molecular Dynamics in Amber: Implementation, Benchmarking and Analysis. 1372-1383 - Lorena Simón-Vidal, Oihane García-Calvo, Uxue Oteo, Sonia Arrasate, Esther Lete, Nuria Sotomayor, Humberto González Díaz:
Perturbation-Theory and Machine Learning (PTML) Model for High-Throughput Screening of Parham Reactions: Experimental and Theoretical Studies. 1384-1396 - Ryuhei Harada, Yasuteru Shigeta:
Temperature-Shuffled Structural Dissimilarity Sampling Based on a Root-Mean-Square Deviation. 1397-1405 - Johanna Hörberg, Patricia Saenz-Méndez, Leif A. Eriksson:
QM/MM Studies of Dph5 - A Promiscuous Methyltransferase in the Eukaryotic Biosynthetic Pathway of Diphthamide. 1406-1414 - Ryan W. Kung, Purshotam Sharma, Stacey D. Wetmore:
Effect of Size and Shape of Nitrogen-Containing Aromatics on Conformational Preferences of DNA Containing Damaged Guanine. 1415-1425 - Sarah E. Graham, Noah Leja, Heather A. Carlson:
MixMD Probeview: Robust Binding Site Prediction from Cosolvent Simulations. 1426-1433 - Scott D. Bembenek, Gavin Hirst, Taraneh Mirzadegan:
Determination of a Focused Mini Kinase Panel for Early Identification of Selective Kinase Inhibitors. 1434-1440 - Andrea Scarpino, György G. Ferenczy, György M. Keserü:
Comparative Evaluation of Covalent Docking Tools. 1441-1458 - Zijuan Zhao, Zhenling Peng, Jianyi Yang:
Improving Sequence-Based Prediction of Protein-Peptide Binding Residues by Introducing Intrinsic Disorder and a Consensus Method. 1459-1468
Volume 58, Number 8, August 2018
- Andrea Volkamer, Sereina Riniker:
Transition from Academia to Industry and Back. 1469-1472 - Phuc-Chau Do, Eric H. Lee, Ly Le:
Steered Molecular Dynamics Simulation in Rational Drug Design. 1473-1482 - Matthew K. Matlock, Tyler B. Hughes, Jayme L. Dahlin, S. Joshua Swamidass:
Modeling Small-Molecule Reactivity Identifies Promiscuous Bioactive Compounds. 1483-1500 - Domenico Gadaleta, Serena Manganelli, Alessandra Roncaglioni, Cosimo Toma, Emilio Benfenati, Enrico Mombelli:
QSAR Modeling of ToxCast Assays Relevant to the Molecular Initiating Events of AOPs Leading to Hepatic Steatosis. 1501-1517 - Ya Chen, Marina Garcia de Lomana, Nils-Ole Friedrich, Johannes Kirchmair:
Characterization of the Chemical Space of Known and Readily Obtainable Natural Products. 1518-1532 - Michael Fernández, Fuqiang Ban, Godwin Woo, Michael Hsing, Takeshi Yamazaki, Eric Leblanc, Paul S. Rennie, William J. Welch, Artem Cherkasov:
Toxic Colors: The Use of Deep Learning for Predicting Toxicity of Compounds Merely from Their Graphic Images. 1533-1543 - Thomas M. Kaiser, Pieter Buys Burger, Christopher J. Butch, Stephen C. Pelly, Dennis Liotta:
A Machine Learning Approach for Predicting HIV Reverse Transcriptase Mutation Susceptibility of Biologically Active Compounds. 1544-1552 - Gurminder Kaur, Elumalai Pavadai, Sergio Wittlin, Kelly Chibale:
3D-QSAR Modeling and Synthesis of New Fusidic Acid Derivatives as Antiplasmodial Agents. 1553-1560 - Ruifeng Liu, Kyle P. Glover, Michael G. Feasel, Anders Wallqvist:
General Approach to Estimate Error Bars for Quantitative Structure-Activity Relationship Predictions of Molecular Activity. 1561-1575 - Rajiv K. Kar, Jeffrey R. Brender, Anirban Ghosh, Anirban Bhunia:
Nonproductive Binding Modes as a Prominent Feature of Aβ40 Fiber Elongation: Insights from Molecular Dynamics Simulation. 1576-1586 - Yang Li, Xianwei Wang, Longlong Ren, Xuecheng Cao, Changge Ji, Fei Xia, John Z. H. Zhang:
Electrostatic Polarization Effect on Cooperative Aggregation of Full Length Human Islet Amyloid. 1587-1595 - Javier Vázquez, Alessandro Deplano, Albert Herrero, Tiziana Ginex, Enric Gibert, Obdulia Rabal, Julen Oyarzabal, Enric Herrero, F. Javier Luque:
Development and Validation of Molecular Overlays Derived from Three-Dimensional Hydrophobic Similarity with PharmScreen. 1596-1609 - Krishna Gopal Chattaraj, Sandip Paul:
Understanding of Structure and Thermodynamics of Melamine Association in Aqueous Solution from a Unified Theoretical and Experimental Approach. 1610-1624 - Eva Nittinger, Florian Flachsenberg, Stefan Bietz, Gudrun Lange, Robert Klein, Matthias Rarey:
Placement of Water Molecules in Protein Structures: From Large-Scale Evaluations to Single-Case Examples. 1625-1637 - Manish Kesherwani, Kutumbarao N. H. V, Devadasan Velmurugan:
Conformational Dynamics of thiM Riboswitch To Understand the Gene Regulation Mechanism Using Markov State Modeling and the Residual Fluctuation Network Approach. 1638-1651 - Na Liu, Wenfang Zhou, Yue Guo, Junmei Wang, Weitao Fu, Huiyong Sun, Dan Li, Mojie Duan, Tingjun Hou:
Molecular Dynamics Simulations Revealed the Regulation of Ligands to the Interactions between Androgen Receptor and Its Coactivator. 1652-1661 - Xiaodong Ren, Yu-Sheng Shi, Yan Zhang, Bin Liu, Li-Hong Zhang, Yu-Bo Peng, Rui Zeng:
Novel Consensus Docking Strategy to Improve Ligand Pose Prediction. 1662-1668 - Haiyang Zhang, Yang Jiang, Ziheng Cui, Chunhua Yin:
Force Field Benchmark of Amino Acids. 2. Partition Coefficients between Water and Organic Solvents. 1669-1681 - David C. B. Siebert, Marcus Wieder, Lydia Schlener, Petra Scholze, Stefan Boresch, Thierry Langer, Michael Schnürch, Marko D. Mihovilovic, Lars Richter, Margot Ernst, Gerhard F. Ecker:
SAR-Guided Scoring Function and Mutational Validation Reveal the Binding Mode of CGS-8216 at the α1+/γ2- Benzodiazepine Site. 1682-1696 - Thomas Gaillard:
Evaluation of AutoDock and AutoDock Vina on the CASF-2013 Benchmark. 1697-1706 - Martin Kotev, Rosalia Pascual, Carmen Almansa, Victor Guallar, Robert Soliva:
Pushing the Limits of Computational Structure-Based Drug Design with a Cryo-EM Structure: The Ca2+ Channel α2δ-1 Subunit as a Test Case. 1707-1715 - Christian Margreitter, Chris Oostenbrink:
Correction to Optimization of Protein Backbone Dihedral Angles by Means of Hamiltonian Reweighting. 1716-1720 - Sergio Decherchi, Giovanni Bottegoni, Andrea Spitaleri, Walter Rocchia, Andrea Cavalli:
Addendum to BiKi Life Sciences: A New Suite for Molecular Dynamics and Related Methods in Drug Discovery. 1721
Volume 58, Number 9, September 2018
- Sepp Hochreiter, Günter Klambauer, Matthias Rarey:
Machine Learning in Drug Discovery. 1723-1724 - Jing-Fang Yang, Fan Wang, Wen Jiang, Guangyou Zhou, Cheng-Zhang Li, Xiao-Lei Zhu, Ge-Fei Hao, Guangfu Yang:
PADFrag: A Database Built for the Exploration of Bioactive Fragment Space for Drug Discovery. 1725-1730 - Daniel Probst, Jean-Louis Reymond:
Exploring DrugBank in Virtual Reality Chemical Space. 1731-1735 - Kristina Preuer, Philipp Renz, Thomas Unterthiner, Sepp Hochreiter, Günter Klambauer:
Fréchet ChemNet Distance: A Metric for Generative Models for Molecules in Drug Discovery. 1736-1741 - Lauren Takahashi, Itsuki Miyazato, Keisuke Takahashi:
Redesigning the Materials and Catalysts Database Construction Process Using Ontologies. 1742-1754 - Robert M. Hanson, Sophia Musacchio, John W. Mayfield, Mikko J. Vainio, Andrey Yerin, Dmitry Redkin:
Algorithmic Analysis of Cahn-Ingold-Prelog Rules of Stereochemistry: Proposals for Revised Rules and a Guide for Machine Implementation. 1755-1765 - Alexander D. Wade, Lee-Ping Wang, David J. Huggins:
Assimilating Radial Distribution Functions To Build Water Models with Improved Structural Properties. 1766-1778 - Maximiliano Riquelme, Alejandro Lara, David L. Mobley, Toon Verstraelen, Adelio R. Matamala, Esteban Vöhringer-Martinez:
Hydration Free Energies in the FreeSolv Database Calculated with Polarized Iterative Hirshfeld Charges. 1779-1797 - Irene Luque Ruiz, Miguel Ángel Gómez-Nieto:
Study of Data Set Modelability: Modelability, Rivality, and Weighted Modelability Indexes. 1798-1814 - Stefano Curcio, Francesco Petrosino, M. Morrone, Giorgio De Luca:
Interactions between Proteins and the Membrane Surface in Multiscale Modeling of Organic Fouling. 1815-1827 - W. M. C. Sameera, Feliu Maseras:
Expanding the Range of Force Fields Available for ONIOM Calculations: The SICTWO Interface. 1828-1835 - Arshad Mehmood, Stephanie I. Jones, Peng Tao, Benjamin G. Janesko:
An Orbital-Overlap Complement to Ligand and Binding Site Electrostatic Potential Maps. 1836-1846 - Vishal B. Siramshetty, Robert Preissner, Björn-Oliver Gohlke:
Exploring Activity Profiles of PAINS and Their Structural Context in Target-Ligand Complexes. 1847-1857 - Srijita Paul, Sandip Paul:
How Does Aqueous Choline-O-Sulfate Solution Nullify the Action of Urea in Protein Denaturation? 1858-1869 - Kathryn A. Giblin, Samantha J. Hughes, Helen Boyd, Pia Hansson, Andreas Bender:
Prospectively Validated Proteochemometric Models for the Prediction of Small-Molecule Binding to Bromodomain Proteins. 1870-1888 - Amika Sood, Oksana O. Gerlits, Ye Ji, Nicolai V. Bovin, Leighton Coates, Robert J. Woods:
Defining the Specificity of Carbohydrate-Protein Interactions by Quantifying Functional Group Contributions. 1889-1901 - Joon S. Kang, Antonia L. Zhang, Mohammad Faheem, Charles J. Zhang, Ni Ai, John D. Buynak, William J. Welsh, Peter Oelschlaeger:
Virtual Screening and Experimental Testing of B1 Metallo-β-lactamase Inhibitors. 1902-1914 - Bing Xie, John D. Clark, David D. L. Minh:
Efficiency of Stratification for Ensemble Docking Using Reduced Ensembles. 1915-1925 - Rui Lai, Wei-Jen Tang, Hui Li:
Catalytic Mechanism of Amyloid-β Peptide Degradation by Insulin Degrading Enzyme: Insights from Quantum Mechanics and Molecular Mechanics Style Møller-Plesset Second Order Perturbation Theory Calculation. 1926-1934 - Ernest Awoonor-Williams, Christopher N. Rowley:
How Reactive are Druggable Cysteines in Protein Kinases? 1935-1946 - Mustafa Tekpinar, Ahmet Yildirim:
Only a Subset of Normal Modes is Sufficient to Identify Linear Correlations in Proteins. 1947-1961 - André Fischer, Charleen G. Don, Martin Smiesko:
Molecular Dynamics Simulations Reveal Structural Differences among Allelic Variants of Membrane-Anchored Cytochrome P450 2D6. 1962-1975 - Tamir Dingjan, Émilie Gillon, Anne Imberty, Serge Pérez, Alexander Titz, Paul A. Ramsland, Elizabeth Yuriev:
Virtual Screening Against Carbohydrate-Binding Proteins: Evaluation and Application to BacterialBurkholderia ambifariaLectin. 1976-1989 - Menyhárt-Botond Sárosi, Terry P. Lybrand:
Molecular Dynamics Simulation of Cyclooxygenase-2 Complexes with Indomethacin closo-Carborane Analogs. 1990-1999 - Isidro Cortés-Ciriano, Nicholas C. Firth, Andreas Bender, Oliver P. Watson:
Discovering Highly Potent Molecules from an Initial Set of Inactives Using Iterative Screening. 2000-2014 - Bianca Villavicencio, Rodrigo Ligabue-Braun, Hugo Verli:
All-Hydrocarbon Staples and Their Effect over Peptide Conformation under Different Force Fields. 2015-2023 - Wenying Yan, Guang Hu, Zhongjie Liang, Jianhong Zhou, Yang Yang, Jiajia Chen, Bairong Shen:
Node-Weighted Amino Acid Network Strategy for Characterization and Identification of Protein Functional Residues. 2024-2032 - Jaswinder Singh, Jack Hanson, Rhys Heffernan, Kuldip K. Paliwal, Yuedong Yang, Yaoqi Zhou:
Detecting Proline and Non-Proline Cis Isomers in Protein Structures from Sequences Using Deep Residual Ensemble Learning. 2033-2042
Volume 58, Number 10, October 2018
- Tai-Sung Lee, David S. Cerutti, Dan Mermelstein, Charles Lin, Scott LeGrand, Timothy J. Giese, Adrian E. Roitberg, David A. Case, Ross C. Walker, Darrin M. York:
GPU-Accelerated Molecular Dynamics and Free Energy Methods in Amber18: Performance Enhancements and New Features. 2043-2050 - Hongbin Yang, Lixia Sun, Zhuang Wang, Weihua Li, Guixia Liu, Yun Tang:
ADMETopt: A Web Server for ADMET Optimization in Drug Design via Scaffold Hopping. 2051-2056 - Arjun Saha, Teena Varghese, Annie Liu, Samantha J. Allen, Taraneh Mirzadegan, Michael D. Hack:
An Analysis of Different Components of a High-Throughput Screening Library. 2057-2068 - Irene Luque Ruiz, Miguel Ángel Gómez-Nieto:
Regression Modelability Index: A New Index for Prediction of the Modelability of Data Sets in the Development of QSAR Regression Models. 2069-2084 - Jill F. Ellenbarger, Inna V. Krieger, Hsiao-Ling Huang, Silvia Gómez-Coca, Thomas R. Ioerger, James C. Sacchettini, Steven E. Wheeler, Kim R. Dunbar:
Anion-π Interactions in Computer-Aided Drug Design: Modeling the Inhibition of Malate Synthase by Phenyl-Diketo Acids. 2085-2091 - Martin Brehm, Martin Thomas:
An Efficient Lossless Compression Algorithm for Trajectories of Atom Positions and Volumetric Data. 2092-2107 - Dominik Budday, Sigrid Leyendecker, Henry van den Bedem:
Kinematic Flexibility Analysis: Hydrogen Bonding Patterns Impart a Spatial Hierarchy of Protein Motion. 2108-2122 - Lingyun Wang, Feng Yan:
Trans and Cis Conformations of the Antihypertensive Drug Valsartan Respectively Lock the Inactive and Active-like States of Angiotensin II Type 1 Receptor: A Molecular Dynamics Study. 2123-2130 - Steve Agajanian, Oluyemi Odeyemi, Nathaniel Bischoff, Simrath Ratra, Gennady M. Verkhivker:
Machine Learning Classification and Structure-Functional Analysis of Cancer Mutations Reveal Unique Dynamic and Network Signatures of Driver Sites in Oncogenes and Tumor Suppressor Genes. 2131-2150 - Carmen Esposito, L. Wiedmer, Amedeo Caflisch:
In Silico Identification of JMJD3 Demethylase Inhibitors. 2151-2163 - Tamas Lazar, Mainak Guharoy, Éva Schád, Peter Tompa:
Unique Physicochemical Patterns of Residues in Protein-Protein Interfaces. 2164-2173
Volume 58, Number 11, November 2018
- Habibah A. Wahab, Rommie E. Amaro, Zoe Cournia:
Women in Computational Chemistry. 2175-2177 - Thibault Tubiana, Jean-Charles Carvaillo, Yves Boulard, Stéphane Bressanelli:
TTClust: A Versatile Molecular Simulation Trajectory Clustering Program with Graphical Summaries. 2178-2182 - Matthew R. Masters, Amr H. Mahmoud, Ying Yang, Markus A. Lill:
Efficient and Accurate Hydration Site Profiling for Enclosed Binding Sites. 2183-2188 - Reda Rawi, Chen-Hsiang Shen, Peter D. Kwong, Gwo-Yu Chuang:
CRISPro: An Automated Pipeline for Protein Conformation Stabilization by Proline. 2189-2192 - Kenneth Goossens, Hans De Winter:
Molecular Dynamics Simulations of Membrane Proteins: An Overview. 2193-2202 - Yen S. Low, Vinicius M. Alves, Denis Fourches, Alexander Sedykh, Carolina Horta Andrade, Eugene N. Muratov, Ivan Rusyn, Alexander Tropsha:
Chemistry-Wide Association Studies (CWAS): A Novel Framework for Identifying and Interpreting Structure-Activity Relationships. 2203-2213 - Sonia Zulfiqar, M. Farooq Wahab, Muhammad Ilyas Sarwar, Ingo Lieberwirth:
Is Machine Translation a Reliable Tool for Reading German Scientific Databases and Research Articles? 2214-2223 - Rafal Kurczab, Pawel Sliwa, Krzysztof Rataj, Rafal Kafel, Andrzej J. Bojarski:
Salt Bridge in Ligand-Protein Complexes - Systematic Theoretical and Statistical Investigations. 2224-2238 - Yongna Yuan, Zhuangzhuang Zhang, Matthew J. L. Mills, Rongjing Hu, Ruisheng Zhang:
Assessing Force Field Potential Energy Function Accuracy via a Multipolar Description of Atomic Electrostatic Interactions in RNA. 2239-2254 - Mattia Bernetti, Elena Rosini, Luca Mollica, Matteo Masetti, Loredano Pollegioni, Maurizio Recanatini, Andrea Cavalli:
Binding Residence Time through Scaled Molecular Dynamics: A Prospective Application to hDAAO Inhibitors. 2255-2265 - Radha Charan Dash, Zuleyha Ozen, Alessandro A. Rizzo, Socheata Lim, Dmitry M. Korzhnev, M. Kyle Hadden:
Structural Approach To Identify a Lead Scaffold That Targets the Translesion Synthesis Polymerase Rev1. 2266-2277 - Letizia Chiodo, Thérèse E. Malliavin, Sergio Giuffrida, Luca Maragliano, Grazia Cottone:
Closed-Locked and Apo-Resting State Structures of the Human α7 Nicotinic Receptor: A Computational Study. 2278-2293 - Flávia Camila Vieira da Silva, Viviane Veiga do Nascimento, Olga Lima Tavares Machado, Lídia da Silva Pereira, Valdirene Moreira Gomes, André de Oliveira Carvalho:
Insight into the α-Amylase Inhibitory Activity of Plant Lipid Transfer Proteins. 2294-2304 - Daniel Markthaler, Hamzeh Kraus, Niels Hansen:
Overcoming Convergence Issues in Free-Energy Calculations of Amide-to-Ester Mutations in the Pin1-WW Domain. 2305-2318 - Fergus Imrie, Anthony R. Bradley, Mihaela van der Schaar, Charlotte M. Deane:
Protein Family-Specific Models Using Deep Neural Networks and Transfer Learning Improve Virtual Screening and Highlight the Need for More Data. 2319-2330 - Xuben Hou, David Rooklin, Duxiao Yang, Xiao Liang, Kangshuai Li, Jianing Lu, Cheng Wang, Peng Xiao, Yingkai Zhang, Jin-peng Sun, Hao Fang:
Computational Strategy for Bound State Structure Prediction in Structure-Based Virtual Screening: A Case Study of Protein Tyrosine Phosphatase Receptor Type O Inhibitors. 2331-2342 - Hongyi Zhou, Hongnan Cao, Jeffrey Skolnick:
FINDSITEcomb2.0: A New Approach for Virtual Ligand Screening of Proteins and Virtual Target Screening of Biomolecules. 2343-2354 - Maud Jusot, Dirk Stratmann, Marc Vaisset, Jacques Chomilier, Juan Cortés:
Exhaustive Exploration of the Conformational Landscape of Small Cyclic Peptides Using a Robotics Approach. 2355-2368 - Jack Hanson, Kuldip K. Paliwal, Yaoqi Zhou:
Accurate Single-Sequence Prediction of Protein Intrinsic Disorder by an Ensemble of Deep Recurrent and Convolutional Architectures. 2369-2376
Volume 58, Number 12, December 2018
- Hanoch Senderowitz, Alexander Tropsha:
Materials Informatics. 2377-2379 - Alexios Chatzigoulas, Konstantina Karathanou, Dimitris Dellis, Zoe Cournia:
NanoCrystal: A Web-Based Crystallographic Tool for the Construction of Nanoparticles Based on Their Crystal Habit. 2380-2386 - Marcin Miklitz, Kim E. Jelfs:
pywindow: Automated Structural Analysis of Molecular Pores. 2387-2391 - Kevin Tran, Aini Palizhati, Seoin Back, Zachary W. Ulissi:
Dynamic Workflows for Routine Materials Discovery in Surface Science. 2392-2400 - Liang Cao, Chenyang Li, Tim Mueller:
The Use of Cluster Expansions To Predict the Structures and Properties of Surfaces and Nanostructured Materials. 2401-2413 - Vincent Blay, Toshiyuki Yokoi, Humberto González Díaz:
Perturbation Theory-Machine Learning Study of Zeolite Materials Desilication. 2414-2419 - Li Shi, Dongping Chang, Xiaobo Ji, Wencong Lu:
Using Data Mining To Search for Perovskite Materials with Higher Specific Surface Area. 2420-2427 - Omer Kaspi, Abraham Yosipof, Hanoch Senderowitz:
Visualization of Solar Cell Library Space by Dimensionality Reduction Methods. 2428-2439 - Shao-Yu Lu, Sukrit Mukhopadhyay, Robert Froese, Paul M. Zimmerman:
Virtual Screening of Hole Transport, Electron Transport, and Host Layers for Effective OLED Design. 2440-2449 - Liam Wilbraham, Enrico Berardo, Lukas Turcani, Kim E. Jelfs, Martijn A. Zwijnenburg:
High-Throughput Screening Approach for the Optoelectronic Properties of Conjugated Polymers. 2450-2459 - Fleur Legrain, Ambroise van Roekeghem, Stefano Curtarolo, Jesús Carrete, Georg K. H. Madsen, Natalio Mingo:
Vibrational Properties of Metastable Polymorph Structures by Machine Learning. 2460-2466 - Maciej Barycki, Anita Sosnowska, Karolina Jagiello, Tomasz Puzyn:
Multi-Objective Genetic Algorithm (MOGA) As a Feature Selecting Strategy in the Development of Ionic Liquids' Quantitative Toxicity-Toxicity Relationship Models. 2467-2476 - Corey Oses, Eric Gossett, David Hicks, Frisco Rose, Michael J. Mehl, Eric Perim, Ichiro Takeuchi, Stefano Sanvito, Matthias Scheffler, Yoav Lederer, Ohad Levy, Cormac Toher, Stefano Curtarolo:
AFLOW-CHULL: Cloud-Oriented Platform for Autonomous Phase Stability Analysis. 2477-2490 - Nicholas Wagner, Danilo Puggioni, James M. Rondinelli:
Learning from Correlations Based on Local Structure: Rare-Earth Nickelates Revisited. 2491-2501 - Zheng Gong, Yanze Wu, Liang Wu, Huai Sun:
Predicting Thermodynamic Properties of Alkanes by High-Throughput Force Field Simulation and Machine Learning. 2502-2516 - Shaikh Parwaiz, Owais Ahmed Malik, Debabrata Pradhan, Mohammad Mansoob Khan:
Machine-Learning-Based Cyclic Voltammetry Behavior Model for Supercapacitance of Co-Doped Ceria/rGO Nanocomposite. 2517-2527 - Hiromasa Kaneko:
Sparse Generative Topographic Mapping for Both Data Visualization and Clustering. 2528-2535
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