Computational Drug Discovery Methods

Most cited papers

1. A short history of SHELXActa Crystallographica Section A Foundations of Crystallography · 2007 · 87,967 citations
2. AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreadingJournal of Computational Chemistry · 2009 · 38,969 citations
3. AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibilityJournal of Computational Chemistry · 2009 · 26,013 citations
4. SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small moleculesScientific Reports · 2017 · 18,341 citations
5. Overview of the CCP 4 suite and current developmentsActa Crystallographica Section D Biological Crystallography · 2011 · 12,716 citations
6. Comprehensive molecular portraits of human breast tumoursNature · 2012 · 12,671 citations
7. Open Babel: An open chemical toolboxJournal of Cheminformatics · 2011 · 11,515 citations
8. Correlation Coefficients: Appropriate Use and InterpretationAnesthesia & Analgesia · 2018 · 11,076 citations
9. Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy functionJournal of Computational Chemistry · 1998 · 10,968 citations
10. In silico prediction of protein-protein interactions in human macrophagesBMC Research Notes · 2014 · 10,920 citations
11. The Cambridge Structural DatabaseActa Crystallographica Section B Structural Science Crystal Engineering and Materials · 2016 · 10,373 citations
12. Glide: A New Approach for Rapid, Accurate Docking and Scoring. 1. Method and Assessment of Docking AccuracyJournal of Medicinal Chemistry · 2004 · 10,203 citations
13. The STRING database in 2023: protein–protein association networks and functional enrichment analyses for any sequenced genome of interestNucleic Acids Research · 2022 · 9,910 citations
14. DrugBank 5.0: a major update to the DrugBank database for 2018Nucleic Acids Research · 2017 · 9,040 citations
15. Patterns in Hydrogen Bonding: Functionality and Graph Set Analysis in CrystalsAngewandte Chemie International Edition in English · 1995 · 8,238 citations
16. Extended-Connectivity FingerprintsJournal of Chemical Information and Modeling · 2010 · 8,040 citations
17. GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkitBioinformatics · 2013 · 7,748 citations
18. AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python BindingsJournal of Chemical Information and Modeling · 2021 · 7,558 citations
19. Natural Products as Sources of New Drugs over the Nearly Four Decades from 01/1981 to 09/2019Journal of Natural Products · 2020 · 7,154 citations
20. cytoHubba: identifying hub objects and sub-networks from complex interactomeBMC Systems Biology · 2014 · 7,051 citations
21. A Simple Statistical Parameter for Use in Evaluation and Validation of High Throughput Screening AssaysSLAS DISCOVERY · 1999 · 7,043 citations
22. Extra Precision Glide: Docking and Scoring Incorporating a Model of Hydrophobic Enclosure for Protein−Ligand ComplexesJournal of Medicinal Chemistry · 2006 · 7,040 citations
23. LigPlot+: Multiple Ligand–Protein Interaction Diagrams for Drug DiscoveryJournal of Chemical Information and Modeling · 2011 · 6,739 citations
24. The path of chemical reactions - the IRC approachAccounts of Chemical Research · 1981 · 6,701 citations
25. A simple practice guide for dose conversion between animals and humanJournal of Basic and Clinical Pharmacy · 2016 · 6,196 citations
26. Alzheimer's Disease: Genes, Proteins, and TherapyPhysiological Reviews · 2001 · 6,114 citations
27. Drug Combination Studies and Their Synergy Quantification Using the Chou-Talalay MethodCancer Research · 2010 · 5,875 citations
28. pkCSM: Predicting Small-Molecule Pharmacokinetic and Toxicity Properties Using Graph-Based SignaturesJournal of Medicinal Chemistry · 2015 · 5,779 citations
29. The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinitiesExpert Opinion on Drug Discovery · 2015 · 5,668 citations
30. PubChem Substance and Compound databasesNucleic Acids Research · 2015 · 5,633 citations
31. The Connectivity Map: Using Gene-Expression Signatures to Connect Small Molecules, Genes, and DiseaseScience · 2006 · 5,554 citations
32. Natural products in drug discovery: advances and opportunitiesNature Reviews Drug Discovery · 2021 · 5,444 citations
33. Glide: A New Approach for Rapid, Accurate Docking and Scoring. 2. Enrichment Factors in Database ScreeningJournal of Medicinal Chemistry · 2004 · 5,354 citations
34. TCMSP: a database of systems pharmacology for drug discovery from herbal medicinesJournal of Cheminformatics · 2014 · 5,199 citations
35. g_mmpbsa —A GROMACS Tool for High-Throughput MM-PBSA CalculationsJournal of Chemical Information and Modeling · 2014 · 4,955 citations
36. PRODRG: a tool for high-throughput crystallography of protein–ligand complexesActa Crystallographica Section D Biological Crystallography · 2004 · 4,855 citations
37. PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical p K a PredictionsJournal of Chemical Theory and Computation · 2011 · 4,714 citations
38. SwissTargetPrediction: updated data and new features for efficient prediction of protein targets of small moleculesNucleic Acids Research · 2019 · 4,628 citations
39. Encoding and decoding hydrogen-bond patterns of organic compoundsAccounts of Chemical Research · 1990 · 4,605 citations
40. Escape from Flatland: Increasing Saturation as an Approach to Improving Clinical SuccessJournal of Medicinal Chemistry · 2009 · 4,605 citations
41. Correlative Memory Deficits, Aβ Elevation, and Amyloid Plaques in Transgenic MiceScience · 1996 · 4,251 citations
42. New Substructure Filters for Removal of Pan Assay Interference Compounds (PAINS) from Screening Libraries and for Their Exclusion in BioassaysJournal of Medicinal Chemistry · 2010 · 4,078 citations
43. β-Secretase Cleavage of Alzheimer's Amyloid Precursor Protein by the Transmembrane Aspartic Protease BACEScience · 1999 · 3,910 citations
44. Diffusible, nonfibrillar ligands derived from Aβ 1–42 are potent central nervous system neurotoxinsProceedings of the National Academy of Sciences · 1998 · 3,550 citations
45. Improved protein–ligand docking using GOLDProteins Structure Function and Bioinformatics · 2003 · 3,115 citations
46. Fast Calculation of Molecular Polar Surface Area as a Sum of Fragment-Based Contributions and Its Application to the Prediction of Drug Transport PropertiesJournal of Medicinal Chemistry · 2000 · 3,114 citations
47. THE TOXICITY OF POISONS APPLIED JOINTLY1Annals of Applied Biology · 1939 · 2,516 citations