These tools will no longer be maintained as of December 31, 2024. Archived website can be found here. PubMed4Hh GitHub repository can be found here. Contact NLM Customer Service if you have questions.
4. An extensive and diverse set of molecular overlays for the validation of pharmacophore programs. Giangreco I; Cosgrove DA; Packer MJ J Chem Inf Model; 2013 Apr; 53(4):852-66. PubMed ID: 23565904 [TBL] [Abstract][Full Text] [Related]
6. Elucidating molecular overlays from pairwise alignments using a genetic algorithm. Jones G; Gao Y; Sage CR J Chem Inf Model; 2009 Jul; 49(7):1847-55. PubMed ID: 19537722 [TBL] [Abstract][Full Text] [Related]
7. Detection of Binding Site Molecular Interaction Field Similarities. Chartier M; Najmanovich R J Chem Inf Model; 2015 Aug; 55(8):1600-15. PubMed ID: 26158641 [TBL] [Abstract][Full Text] [Related]
8. Bioisostere Identification by Determining the Amino Acid Binding Preferences of Common Chemical Fragments. Sato T; Hashimoto N; Honma T J Chem Inf Model; 2017 Dec; 57(12):2938-2947. PubMed ID: 29111727 [TBL] [Abstract][Full Text] [Related]
9. Side chain virtual screening of matched molecular pairs: a PDB-wide and ChEMBL-wide analysis. Baumgartner MP; Evans DA J Comput Aided Mol Des; 2020 Sep; 34(9):953-963. PubMed ID: 32533370 [TBL] [Abstract][Full Text] [Related]
10. Drug-like density: a method of quantifying the "bindability" of a protein target based on a very large set of pockets and drug-like ligands from the Protein Data Bank. Sheridan RP; Maiorov VN; Holloway MK; Cornell WD; Gao YD J Chem Inf Model; 2010 Nov; 50(11):2029-40. PubMed ID: 20977231 [TBL] [Abstract][Full Text] [Related]
11. BioisoIdentifier: an online free tool to investigate local structural replacements from PDB. Zhang T; Sun S; Wang R; Li T; Gan B; Zhang Y J Cheminform; 2024 Jan; 16(1):7. PubMed ID: 38218937 [TBL] [Abstract][Full Text] [Related]
12. Bioisosteric matrices for ligands of serotonin receptors. Warszycki D; Mordalski S; StaroĊ J; Bojarski AJ ChemMedChem; 2015 Apr; 10(4):601-5. PubMed ID: 25772514 [TBL] [Abstract][Full Text] [Related]
13. ProSelection: A Novel Algorithm to Select Proper Protein Structure Subsets for in Silico Target Identification and Drug Discovery Research. Wang N; Wang L; Xie XQ J Chem Inf Model; 2017 Nov; 57(11):2686-2698. PubMed ID: 29016123 [TBL] [Abstract][Full Text] [Related]
14. Refinement of NMR-determined protein structures with database derived mean-force potentials. Wu D; Jernigan R; Wu Z Proteins; 2007 Jul; 68(1):232-42. PubMed ID: 17387736 [TBL] [Abstract][Full Text] [Related]
15. sc-PDB: an annotated database of druggable binding sites from the Protein Data Bank. Kellenberger E; Muller P; Schalon C; Bret G; Foata N; Rognan D J Chem Inf Model; 2006; 46(2):717-27. PubMed ID: 16563002 [TBL] [Abstract][Full Text] [Related]
16. MB-Isoster: A software for bioisosterism simulation. Elias TC; de Oliveira HCB; da Silveira NJF J Comput Chem; 2018 Nov; 39(29):2481-2487. PubMed ID: 30318630 [TBL] [Abstract][Full Text] [Related]
17. Pharmacophore fingerprint-based approach to binding site subpocket similarity and its application to bioisostere replacement. Wood DJ; de Vlieg J; Wagener M; Ritschel T J Chem Inf Model; 2012 Aug; 52(8):2031-43. PubMed ID: 22830492 [TBL] [Abstract][Full Text] [Related]
18. Conformer generation with OMEGA: algorithm and validation using high quality structures from the Protein Databank and Cambridge Structural Database. Hawkins PC; Skillman AG; Warren GL; Ellingson BA; Stahl MT J Chem Inf Model; 2010 Apr; 50(4):572-84. PubMed ID: 20235588 [TBL] [Abstract][Full Text] [Related]