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Top Articles

#TitleJournalYearCitations
1Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichmentsJournal of Computer-Aided Molecular Design20134,278
2Molden: a pre- and post-processing program for molecular and electronic structuresJournal of Computer-Aided Molecular Design20002,851
3MOPAC: A semiempirical molecular orbital programJournal of Computer-Aided Molecular Design19902,572
4Ligand docking and binding site analysis with PyMOL and Autodock/VinaJournal of Computer-Aided Molecular Design20101,566
5Epik: a software program for pK a prediction and protonation state generation for drug-like moleculesJournal of Computer-Aided Molecular Design20071,564
6Empirical 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 Design19971,517
7Virtual Computational Chemistry Laboratory – Design and DescriptionJournal of Computer-Aided Molecular Design20051,270
8Molecular graph convolutions: moving beyond fingerprintsJournal of Computer-Aided Molecular Design20161,056
9DOCK 4.0: search strategies for automated molecular docking of flexible molecule databasesJournal of Computer-Aided Molecular Design20011,040
10Further development and validation of empirical scoring functions for structure-based binding affinity predictionJournal of Computer-Aided Molecular Design20021,036
11PHASE: a new engine for pharmacophore perception, 3D QSAR model development, and 3D database screening: 1. Methodology and preliminary resultsJournal of Computer-Aided Molecular Design2006983
12Distributed automated docking of flexible ligands to proteins: Parallel applications of AutoDock 2.4Journal of Computer-Aided Molecular Design1996916
13The 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 Design1994874
14Towards the comprehensive, rapid, and accurate prediction of the favorable tautomeric states of drug-like molecules in aqueous solutionJournal of Computer-Aided Molecular Design2010796
15The computer program LUDI: A new method for the de novo design of enzyme inhibitorsJournal of Computer-Aided Molecular Design1992752
16VEGA – An open platform to develop chemo-bio-informatics applications, using plug-in architecture and script programmingJournal of Computer-Aided Molecular Design2004646
17PRODRG, a program for generating molecular topologies and unique molecular descriptors from coordinates of small moleculesJournal of Computer-Aided Molecular Design1996613
18Rational selection of training and test sets for the development of validated QSAR modelsJournal of Computer-Aided Molecular Design2003600
19A review of protein-small molecule docking methodsJournal of Computer-Aided Molecular Design2002565
20Property distribution of drug-related chemical databasesJournal of Computer-Aided Molecular Design2000552
21MAB, a generally applicable molecular force field for structure modelling in medicinal chemistryJournal of Computer-Aided Molecular Design1995548
22Scoring noncovalent protein-ligand interactions: A continuous differentiable function tuned to compute binding affinitiesJournal of Computer-Aided Molecular Design1996545
23Surflex-Dock 2.1: Robust performance from ligand energetic modeling, ring flexibility, and knowledge-based searchJournal of Computer-Aided Molecular Design2007525
24Local elevation: A method for improving the searching properties of molecular dynamics simulationJournal of Computer-Aided Molecular Design1994521
25Online chemical modeling environment (OCHEM): web platform for data storage, model development and publishing of chemical informationJournal of Computer-Aided Molecular Design2011479
26QXP: powerful, rapid computer algorithms for structure-based drug designJournal of Computer-Aided Molecular Design1997469
27Fast prediction and visualization of protein binding pockets with PASSJournal of Computer-Aided Molecular Design2000466
28Computer-aided drug design platform using PyMOLJournal of Computer-Aided Molecular Design2011445
29Testing and validation of the Automated Topology Builder (ATB) version 2.0: prediction of hydration free enthalpiesJournal of Computer-Aided Molecular Design2014436
30FRED and HYBRID docking performance on standardized datasetsJournal of Computer-Aided Molecular Design2012413
31LUDI: rule-based automatic design of new substituents for enzyme inhibitor leadsJournal of Computer-Aided Molecular Design1992412
32Ligand binding affinity prediction by linear interaction energy methodsJournal of Computer-Aided Molecular Design1998408
33Predictive QSAR modeling based on diversity sampling of experimental datasets for the training and test set selectionJournal of Computer-Aided Molecular Design2002400
34Guidelines for the analysis of free energy calculationsJournal of Computer-Aided Molecular Design2015398
35Prediction of binding constants of protein ligands: a fast method for the prioritization of hits obtained from de novo design or 3D database search programsJournal of Computer-Aided Molecular Design1998397
36Development and validation of a modular, extensible docking program: DOCK 5Journal of Computer-Aided Molecular Design2006375
37A fast new approach to pharmacophore mapping and its application to dopaminergic and benzodiazepine agonistsJournal of Computer-Aided Molecular Design1993364
38Estimation of the size of drug-like chemical space based on GDB-17 dataJournal of Computer-Aided Molecular Design2013363
39Variability in docking success rates due to dataset preparationJournal of Computer-Aided Molecular Design2012358
40A genetic algorithm for flexible molecular overlay and pharmacophore elucidationJournal of Computer-Aided Molecular Design1995350
41Boltzmann's principle, knowledge-based mean fields and protein folding. An approach to the computational determination of protein structuresJournal of Computer-Aided Molecular Design1993349
42Evaluation 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 Design2008344
43Sample-distance partial least squares: PLS optimized for many variables, with application to CoMFAJournal of Computer-Aided Molecular Design1993341
44AM1-SM2 and PM3-SM3 parameterized SCF solvation models for free energies in aqueous solutionJournal of Computer-Aided Molecular Design1992317
45Maximum common subgraph isomorphism algorithms for the matching of chemical structuresJournal of Computer-Aided Molecular Design2002315
46FreeSolv: a database of experimental and calculated hydration free energies, with input filesJournal of Computer-Aided Molecular Design2014313
47Strategic approaches to drug design. I. An integrated software framework for molecular modellingJournal of Computer-Aided Molecular Design1987311
48Class IV charge models: A new semiempirical approach in quantum chemistryJournal of Computer-Aided Molecular Design1995311
49HINT: A new method of empirical hydrophobic field calculation for CoMFAJournal of Computer-Aided Molecular Design1991306
50Comparative study of several algorithms for flexible ligand dockingJournal of Computer-Aided Molecular Design2003304