ZINCPharmer: Pharmacophore Search of the ZINC Database

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2012 May 4

PMID 22553363

Citations 129

Authors

David Ryan Koes

Carlos J Camacho

Affiliations

Soon will be listed here.

Abstract

ZINCPharmer (http://zincpharmer.csb.pitt.edu) is an online interface for searching the purchasable compounds of the ZINC database using the Pharmer pharmacophore search technology. A pharmacophore describes the spatial arrangement of the essential features of an interaction. Compounds that match a well-defined pharmacophore serve as potential lead compounds for drug discovery. ZINCPharmer provides tools for constructing and refining pharmacophore hypotheses directly from molecular structure. A search of 176 million conformers of 18.3 million compounds typically takes less than a minute. The results can be immediately viewed, or the aligned structures may be downloaded for off-line analysis. ZINCPharmer enables the rapid and interactive search of purchasable chemical space.

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References

Baroni M, Cruciani G, Sciabola S, Perruccio F, Mason J . A common reference framework for analyzing/comparing proteins and ligands. Fingerprints for Ligands and Proteins (FLAP): theory and application. J Chem Inf Model. 2007; 47(2):279-94. DOI: 10.1021/ci600253e. View

Schneidman-Duhovny D, Dror O, Inbar Y, Nussinov R, Wolfson H . PharmaGist: a webserver for ligand-based pharmacophore detection. Nucleic Acids Res. 2008; 36(Web Server issue):W223-8. PMC: 2447755. DOI: 10.1093/nar/gkn187. View

Liu X, Ouyang S, Yu B, Liu Y, Huang K, Gong J . PharmMapper server: a web server for potential drug target identification using pharmacophore mapping approach. Nucleic Acids Res. 2010; 38(Web Server issue):W609-14. PMC: 2896160. DOI: 10.1093/nar/gkq300. View

Kirchmair J, Wolber G, Laggner C, Langer T . Comparative performance assessment of the conformational model generators omega and catalyst: a large-scale survey on the retrieval of protein-bound ligand conformations. J Chem Inf Model. 2006; 46(4):1848-61. DOI: 10.1021/ci060084g. View

Koes D, Camacho C . Small-molecule inhibitor starting points learned from protein-protein interaction inhibitor structure. Bioinformatics. 2012; 28(6):784-91. PMC: 3307105. DOI: 10.1093/bioinformatics/btr717. View

Fang X, Wang S . A web-based 3D-database pharmacophore searching tool for drug discovery. J Chem Inf Comput Sci. 2002; 42(2):192-8. DOI: 10.1021/ci010083i. View

Sheridan R, Kearsley S . Why do we need so many chemical similarity search methods?. Drug Discov Today. 2003; 7(17):903-11. DOI: 10.1016/s1359-6446(02)02411-x. View

Maass P, Schulz-Gasch T, Stahl M, Rarey M . Recore: a fast and versatile method for scaffold hopping based on small molecule crystal structure conformations. J Chem Inf Model. 2007; 47(2):390-9. DOI: 10.1021/ci060094h. View

Langer T, Krovat E . Chemical feature-based pharmacophores and virtual library screening for discovery of new leads. Curr Opin Drug Discov Devel. 2003; 6(3):370-6. View

10.

Wolber G, Langer T . LigandScout: 3-D pharmacophores derived from protein-bound ligands and their use as virtual screening filters. J Chem Inf Model. 2005; 45(1):160-9. DOI: 10.1021/ci049885e. View

11.

Veber D, Johnson S, Cheng H, Smith B, Ward K, Kopple K . Molecular properties that influence the oral bioavailability of drug candidates. J Med Chem. 2002; 45(12):2615-23. DOI: 10.1021/jm020017n. View

12.

Raymond J, Willett P . Maximum common subgraph isomorphism algorithms for the matching of chemical structures. J Comput Aided Mol Des. 2003; 16(7):521-33. DOI: 10.1023/a:1021271615909. View

13.

Hsin K, Morgan H, Shave S, Hinton A, Taylor P, Walkinshaw M . EDULISS: a small-molecule database with data-mining and pharmacophore searching capabilities. Nucleic Acids Res. 2010; 39(Database issue):D1042-8. PMC: 3013767. DOI: 10.1093/nar/gkq878. View

14.

Irwin J, Shoichet B . ZINC--a free database of commercially available compounds for virtual screening. J Chem Inf Model. 2005; 45(1):177-82. PMC: 1360656. DOI: 10.1021/ci049714+. View

15.

Spitzer G, Heiss M, Mangold M, Markt P, Kirchmair J, Wolber G . One concept, three implementations of 3D pharmacophore-based virtual screening: distinct coverage of chemical search space. J Chem Inf Model. 2010; 50(7):1241-7. DOI: 10.1021/ci100136b. View

16.

Mason J, GOOD A, Martin E . 3-D pharmacophores in drug discovery. Curr Pharm Des. 2001; 7(7):567-97. DOI: 10.2174/1381612013397843. View

17.

Koes D, Camacho C . Pharmer: efficient and exact pharmacophore search. J Chem Inf Model. 2011; 51(6):1307-14. PMC: 3124593. DOI: 10.1021/ci200097m. View

18.

Mason J, Cheney D . Library design and virtual screening using multiple 4-point pharmacophore fingerprints. Pac Symp Biocomput. 2000; :576-87. DOI: 10.1142/9789814447331_0055. View

19.

Leach A, Gillet V, Lewis R, Taylor R . Three-dimensional pharmacophore methods in drug discovery. J Med Chem. 2009; 53(2):539-58. DOI: 10.1021/jm900817u. View

20.

OBoyle N, Banck M, James C, Morley C, Vandermeersch T, Hutchison G . Open Babel: An open chemical toolbox. J Cheminform. 2011; 3:33. PMC: 3198950. DOI: 10.1186/1758-2946-3-33. View