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all documents
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Top Articles

#TitleJournalYearCitations
1Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichmentsJournal of Computer-Aided Molecular Design20133,989
2MOPAC: A semiempirical molecular orbital programJournal of Computer-Aided Molecular Design19902,527
3Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexesJournal of Computer-Aided Molecular Design19971,500
4Epik: a software program for pK a prediction and protonation state generation for drug-like moleculesJournal of Computer-Aided Molecular Design20071,454
5Ligand docking and binding site analysis with PyMOL and Autodock/VinaJournal of Computer-Aided Molecular Design20101,410
6Virtual Computational Chemistry Laboratory – Design and DescriptionJournal of Computer-Aided Molecular Design20051,250
7DOCK 4.0: search strategies for automated molecular docking of flexible molecule databasesJournal of Computer-Aided Molecular Design20011,022
8Further development and validation of empirical scoring functions for structure-based binding affinity predictionJournal of Computer-Aided Molecular Design20021,012
9Molecular graph convolutions: moving beyond fingerprintsJournal of Computer-Aided Molecular Design2016991
10PHASE: a new engine for pharmacophore perception, 3D QSAR model development, and 3D database screening: 1. Methodology and preliminary resultsJournal of Computer-Aided Molecular Design2006963
11Distributed automated docking of flexible ligands to proteins: Parallel applications of AutoDock 2.4Journal of Computer-Aided Molecular Design1996907
12The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structureJournal of Computer-Aided Molecular Design1994869
13Towards the comprehensive, rapid, and accurate prediction of the favorable tautomeric states of drug-like molecules in aqueous solutionJournal of Computer-Aided Molecular Design2010748
14The computer program LUDI: A new method for the de novo design of enzyme inhibitorsJournal of Computer-Aided Molecular Design1992745
15VEGA – An open platform to develop chemo-bio-informatics applications, using plug-in architecture and script programmingJournal of Computer-Aided Molecular Design2004635
16PRODRG, a program for generating molecular topologies and unique molecular descriptors from coordinates of small moleculesJournal of Computer-Aided Molecular Design1996596
17Rational selection of training and test sets for the development of validated QSAR modelsJournal of Computer-Aided Molecular Design2003588
18A review of protein-small molecule docking methodsJournal of Computer-Aided Molecular Design2002557
19MAB, a generally applicable molecular force field for structure modelling in medicinal chemistryJournal of Computer-Aided Molecular Design1995541
20Scoring noncovalent protein-ligand interactions: A continuous differentiable function tuned to compute binding affinitiesJournal of Computer-Aided Molecular Design1996539
21Surflex-Dock 2.1: Robust performance from ligand energetic modeling, ring flexibility, and knowledge-based searchJournal of Computer-Aided Molecular Design2007517
22Local elevation: A method for improving the searching properties of molecular dynamics simulationJournal of Computer-Aided Molecular Design1994510
23Online chemical modeling environment (OCHEM): web platform for data storage, model development and publishing of chemical informationJournal of Computer-Aided Molecular Design2011453
24Computer-aided drug design platform using PyMOLJournal of Computer-Aided Molecular Design2011416
25Testing and validation of the Automated Topology Builder (ATB) version 2.0: prediction of hydration free enthalpiesJournal of Computer-Aided Molecular Design2014416
26LUDI: rule-based automatic design of new substituents for enzyme inhibitor leadsJournal of Computer-Aided Molecular Design1992408
27Ligand binding affinity prediction by linear interaction energy methodsJournal of Computer-Aided Molecular Design1998401
28Predictive QSAR modeling based on diversity sampling of experimental datasets for the training and test set selectionJournal of Computer-Aided Molecular Design2002397
29FRED and HYBRID docking performance on standardized datasetsJournal of Computer-Aided Molecular Design2012387
30Guidelines for the analysis of free energy calculationsJournal of Computer-Aided Molecular Design2015375
31Development and validation of a modular, extensible docking program: DOCK 5Journal of Computer-Aided Molecular Design2006373
32A fast new approach to pharmacophore mapping and its application to dopaminergic and benzodiazepine agonistsJournal of Computer-Aided Molecular Design1993363
33A genetic algorithm for flexible molecular overlay and pharmacophore elucidationJournal of Computer-Aided Molecular Design1995350
34Boltzmann's principle, knowledge-based mean fields and protein folding. An approach to the computational determination of protein structuresJournal of Computer-Aided Molecular Design1993347
35Sample-distance partial least squares: PLS optimized for many variables, with application to CoMFAJournal of Computer-Aided Molecular Design1993340
36Variability in docking success rates due to dataset preparationJournal of Computer-Aided Molecular Design2012338
37Evaluation 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 Design2008330
38Estimation of the size of drug-like chemical space based on GDB-17 dataJournal of Computer-Aided Molecular Design2013319
39AM1-SM2 and PM3-SM3 parameterized SCF solvation models for free energies in aqueous solutionJournal of Computer-Aided Molecular Design1992316
40Strategic approaches to drug design. I. An integrated software framework for molecular modellingJournal of Computer-Aided Molecular Design1987310
41Class IV charge models: A new semiempirical approach in quantum chemistryJournal of Computer-Aided Molecular Design1995309
42Maximum common subgraph isomorphism algorithms for the matching of chemical structuresJournal of Computer-Aided Molecular Design2002309
43HINT: A new method of empirical hydrophobic field calculation for CoMFAJournal of Computer-Aided Molecular Design1991303
44Comparative study of several algorithms for flexible ligand dockingJournal of Computer-Aided Molecular Design2003297
45Docking and scoring with ICM: the benchmarking results and strategies for improvementJournal of Computer-Aided Molecular Design2012290
46IsoStar: a library of information about nonbonded interactionsJournal of Computer-Aided Molecular Design1997289
47FreeSolv: a database of experimental and calculated hydration free energies, with input filesJournal of Computer-Aided Molecular Design2014284
48An improved relaxed complex scheme for receptor flexibility in computer-aided drug designJournal of Computer-Aided Molecular Design2008283
49Recommendations for evaluation of computational methodsJournal of Computer-Aided Molecular Design2008269
50Efficient overlay of small organic molecules using 3D pharmacophoresJournal of Computer-Aided Molecular Design2007265