| Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments | 2013/03/01 | English | 3,651 |
| Epik: a software program for pK a prediction and protonation state generation for drug-like molecules | 2007/09/27 | English | 1,336 |
| Ligand docking and binding site analysis with PyMOL and Autodock/Vina | 2010/04/17 | English | 1,295 |
| Virtual Computational Chemistry Laboratory – Design and Description | 2005/06/01 | English | 1,085 |
| PHASE: a new engine for pharmacophore perception, 3D QSAR model development, and 3D database screening: 1. Methodology and preliminary results | 2006/11/24 | English | 812 |
| Molecular graph convolutions: moving beyond fingerprints | 2016/08/01 | English | 748 |
| Towards the comprehensive, rapid, and accurate prediction of the favorable tautomeric states of drug-like molecules in aqueous solution | 2010/03/31 | English | 686 |
| Surflex-Dock 2.1: Robust performance from ligand energetic modeling, ring flexibility, and knowledge-based search | 2007/03/27 | English | 463 |
| Testing and validation of the Automated Topology Builder (ATB) version 2.0: prediction of hydration free enthalpies | 2014/01/30 | English | 394 |
| Online chemical modeling environment (OCHEM): web platform for data storage, model development and publishing of chemical information | 2011/06/01 | English | 389 |
| Computer-aided drug design platform using PyMOL | 2010/10/30 | English | 360 |
| FRED and HYBRID docking performance on standardized datasets | 2012/06/05 | English | 326 |
| Guidelines for the analysis of free energy calculations | 2015/03/26 | English | 325 |
| Evaluation of the performance of 3D virtual screening protocols: RMSD comparisons, enrichment assessments, and decoy selection—What can we learn from earlier mistakes? | 2008/01/15 | English | 287 |
| Variability in docking success rates due to dataset preparation | 2012/05/08 | English | 285 |
| Development and validation of a modular, extensible docking program: DOCK 5 | 2006/12/06 | English | 272 |
| FreeSolv: a database of experimental and calculated hydration free energies, with input files | 2014/06/14 | English | 264 |
| Estimation of the size of drug-like chemical space based on GDB-17 data | 2013/08/01 | English | 263 |
| Docking and scoring with ICM: the benchmarking results and strategies for improvement | 2012/05/09 | English | 237 |
| Recommendations for evaluation of computational methods | 2008/03/01 | English | 219 |
| Interpretation of machine learning models using shapley values: application to compound potency and multi-target activity predictions | 2020/05/02 | English | 219 |
| Efficient overlay of small organic molecules using 3D pharmacophores | 2006/10/19 | English | 212 |
| TargetNet: a web service for predicting potential drug–target interaction profiling via multi-target SAR models | 2016/05/01 | English | 209 |
| A consistent description of HYdrogen bond and DEhydration energies in protein–ligand complexes: methods behind the HYDE scoring function | 2012/12/27 | English | 205 |
| An improved relaxed complex scheme for receptor flexibility in computer-aided drug design | 2008/01/15 | English | 200 |
| Surflex-Dock: Docking benchmarks and real-world application | 2012/05/09 | English | 189 |
| BODIL: a molecular modeling environment for structure-function analysis and drug design | 2004/06/01 | English | 185 |
| The future of molecular dynamics simulations in drug discovery | 2011/12/20 | English | 177 |
| Prediction of protein–ligand binding affinity by free energy simulations: assumptions, pitfalls and expectations | 2010/05/28 | English | 173 |
| Let’s not forget tautomers | 2009/10/01 | English | 169 |