# | Title | Journal | Year | Citations |
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1 | Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments | Journal of Computer-Aided Molecular Design | 2013 | 3,989 |
2 | MOPAC: A semiempirical molecular orbital program | Journal of Computer-Aided Molecular Design | 1990 | 2,527 |
3 | Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes | Journal of Computer-Aided Molecular Design | 1997 | 1,500 |
4 | Epik: a software program for pK a prediction and protonation state generation for drug-like molecules | Journal of Computer-Aided Molecular Design | 2007 | 1,454 |
5 | Ligand docking and binding site analysis with PyMOL and Autodock/Vina | Journal of Computer-Aided Molecular Design | 2010 | 1,410 |
6 | Virtual Computational Chemistry Laboratory – Design and Description | Journal of Computer-Aided Molecular Design | 2005 | 1,250 |
7 | DOCK 4.0: search strategies for automated molecular docking of flexible molecule databases | Journal of Computer-Aided Molecular Design | 2001 | 1,022 |
8 | Further development and validation of empirical scoring functions for structure-based binding affinity prediction | Journal of Computer-Aided Molecular Design | 2002 | 1,012 |
9 | Molecular graph convolutions: moving beyond fingerprints | Journal of Computer-Aided Molecular Design | 2016 | 991 |
10 | PHASE: a new engine for pharmacophore perception, 3D QSAR model development, and 3D database screening: 1. Methodology and preliminary results | Journal of Computer-Aided Molecular Design | 2006 | 963 |
11 | Distributed automated docking of flexible ligands to proteins: Parallel applications of AutoDock 2.4 | Journal of Computer-Aided Molecular Design | 1996 | 907 |
12 | The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure | Journal of Computer-Aided Molecular Design | 1994 | 869 |
13 | Towards the comprehensive, rapid, and accurate prediction of the favorable tautomeric states of drug-like molecules in aqueous solution | Journal of Computer-Aided Molecular Design | 2010 | 748 |
14 | The computer program LUDI: A new method for the de novo design of enzyme inhibitors | Journal of Computer-Aided Molecular Design | 1992 | 745 |
15 | VEGA – An open platform to develop chemo-bio-informatics applications, using plug-in architecture and script programming | Journal of Computer-Aided Molecular Design | 2004 | 635 |
16 | PRODRG, a program for generating molecular topologies and unique molecular descriptors from coordinates of small molecules | Journal of Computer-Aided Molecular Design | 1996 | 596 |
17 | Rational selection of training and test sets for the development of validated QSAR models | Journal of Computer-Aided Molecular Design | 2003 | 588 |
18 | A review of protein-small molecule docking methods | Journal of Computer-Aided Molecular Design | 2002 | 557 |
19 | MAB, a generally applicable molecular force field for structure modelling in medicinal chemistry | Journal of Computer-Aided Molecular Design | 1995 | 541 |
20 | Scoring noncovalent protein-ligand interactions: A continuous differentiable function tuned to compute binding affinities | Journal of Computer-Aided Molecular Design | 1996 | 539 |
21 | Surflex-Dock 2.1: Robust performance from ligand energetic modeling, ring flexibility, and knowledge-based search | Journal of Computer-Aided Molecular Design | 2007 | 517 |
22 | Local elevation: A method for improving the searching properties of molecular dynamics simulation | Journal of Computer-Aided Molecular Design | 1994 | 510 |
23 | Online chemical modeling environment (OCHEM): web platform for data storage, model development and publishing of chemical information | Journal of Computer-Aided Molecular Design | 2011 | 453 |
24 | Computer-aided drug design platform using PyMOL | Journal of Computer-Aided Molecular Design | 2011 | 416 |
25 | Testing and validation of the Automated Topology Builder (ATB) version 2.0: prediction of hydration free enthalpies | Journal of Computer-Aided Molecular Design | 2014 | 416 |
26 | LUDI: rule-based automatic design of new substituents for enzyme inhibitor leads | Journal of Computer-Aided Molecular Design | 1992 | 408 |
27 | Ligand binding affinity prediction by linear interaction energy methods | Journal of Computer-Aided Molecular Design | 1998 | 401 |
28 | Predictive QSAR modeling based on diversity sampling of experimental datasets for the training and test set selection | Journal of Computer-Aided Molecular Design | 2002 | 397 |
29 | FRED and HYBRID docking performance on standardized datasets | Journal of Computer-Aided Molecular Design | 2012 | 387 |
30 | Guidelines for the analysis of free energy calculations | Journal of Computer-Aided Molecular Design | 2015 | 375 |
31 | Development and validation of a modular, extensible docking program: DOCK 5 | Journal of Computer-Aided Molecular Design | 2006 | 373 |
32 | A fast new approach to pharmacophore mapping and its application to dopaminergic and benzodiazepine agonists | Journal of Computer-Aided Molecular Design | 1993 | 363 |
33 | A genetic algorithm for flexible molecular overlay and pharmacophore elucidation | Journal of Computer-Aided Molecular Design | 1995 | 350 |
34 | Boltzmann's principle, knowledge-based mean fields and protein folding. An approach to the computational determination of protein structures | Journal of Computer-Aided Molecular Design | 1993 | 347 |
35 | Sample-distance partial least squares: PLS optimized for many variables, with application to CoMFA | Journal of Computer-Aided Molecular Design | 1993 | 340 |
36 | Variability in docking success rates due to dataset preparation | Journal of Computer-Aided Molecular Design | 2012 | 338 |
37 | Evaluation of the performance of 3D virtual screening protocols: RMSD comparisons, enrichment assessments, and decoy selection—What can we learn from earlier mistakes? | Journal of Computer-Aided Molecular Design | 2008 | 330 |
38 | Estimation of the size of drug-like chemical space based on GDB-17 data | Journal of Computer-Aided Molecular Design | 2013 | 319 |
39 | AM1-SM2 and PM3-SM3 parameterized SCF solvation models for free energies in aqueous solution | Journal of Computer-Aided Molecular Design | 1992 | 316 |
40 | Strategic approaches to drug design. I. An integrated software framework for molecular modelling | Journal of Computer-Aided Molecular Design | 1987 | 310 |
41 | Class IV charge models: A new semiempirical approach in quantum chemistry | Journal of Computer-Aided Molecular Design | 1995 | 309 |
42 | Maximum common subgraph isomorphism algorithms for the matching of chemical structures | Journal of Computer-Aided Molecular Design | 2002 | 309 |
43 | HINT: A new method of empirical hydrophobic field calculation for CoMFA | Journal of Computer-Aided Molecular Design | 1991 | 303 |
44 | Comparative study of several algorithms for flexible ligand docking | Journal of Computer-Aided Molecular Design | 2003 | 297 |
45 | Docking and scoring with ICM: the benchmarking results and strategies for improvement | Journal of Computer-Aided Molecular Design | 2012 | 290 |
46 | IsoStar: a library of information about nonbonded interactions | Journal of Computer-Aided Molecular Design | 1997 | 289 |
47 | FreeSolv: a database of experimental and calculated hydration free energies, with input files | Journal of Computer-Aided Molecular Design | 2014 | 284 |
48 | An improved relaxed complex scheme for receptor flexibility in computer-aided drug design | Journal of Computer-Aided Molecular Design | 2008 | 283 |
49 | Recommendations for evaluation of computational methods | Journal of Computer-Aided Molecular Design | 2008 | 269 |
50 | Efficient overlay of small organic molecules using 3D pharmacophores | Journal of Computer-Aided Molecular Design | 2007 | 265 |