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Items: 1 to 20 of 84

1.

Functional prediction of binding pockets.

Kontoyianni M, Rosnick CB.

J Chem Inf Model. 2012 Mar 26;52(3):824-33. doi: 10.1021/ci2005912. Epub 2012 Mar 7.

PMID:
22352431
2.

From the similarity analysis of protein cavities to the functional classification of protein families using cavbase.

Kuhn D, Weskamp N, Schmitt S, Hüllermeier E, Klebe G.

J Mol Biol. 2006 Jun 16;359(4):1023-44. Epub 2006 Apr 25.

PMID:
16697007
3.

A new protein binding pocket similarity measure based on comparison of clouds of atoms in 3D: application to ligand prediction.

Hoffmann B, Zaslavskiy M, Vert JP, Stoven V.

BMC Bioinformatics. 2010 Feb 22;11:99. doi: 10.1186/1471-2105-11-99.

4.

Merging chemical and biological space: Structural mapping of enzyme binding pocket space.

Weskamp N, Hüllermeier E, Klebe G.

Proteins. 2009 Aug 1;76(2):317-30. doi: 10.1002/prot.22345.

PMID:
19173307
5.

Prediction of sub-cavity binding preferences using an adaptive physicochemical structure representation.

Wallach I, Lilien RH.

Bioinformatics. 2009 Jun 15;25(12):i296-304. doi: 10.1093/bioinformatics/btp204.

6.

PatchSurfers: Two methods for local molecular property-based binding ligand prediction.

Shin WH, Bures MG, Kihara D.

Methods. 2016 Jan 15;93:41-50. doi: 10.1016/j.ymeth.2015.09.026. Epub 2015 Sep 30.

7.

Real-time ligand binding pocket database search using local surface descriptors.

Chikhi R, Sael L, Kihara D.

Proteins. 2010 Jul;78(9):2007-28. doi: 10.1002/prot.22715.

8.

[Development and validation of programs for ligand-binding-pocket search].

Oda A.

Yakugaku Zasshi. 2011;131(10):1429-35. Review. Japanese.

9.

Large-scale mining for similar protein binding pockets: with RAPMAD retrieval on the fly becomes real.

Krotzky T, Grunwald C, Egerland U, Klebe G.

J Chem Inf Model. 2015 Jan 26;55(1):165-79. doi: 10.1021/ci5005898. Epub 2014 Dec 18.

PMID:
25474400
10.

A comprehensive survey of small-molecule binding pockets in proteins.

Gao M, Skolnick J.

PLoS Comput Biol. 2013 Oct;9(10):e1003302. doi: 10.1371/journal.pcbi.1003302. Epub 2013 Oct 24.

11.

Predicting gene ontology functions from protein's regional surface structures.

Liu ZP, Wu LY, Wang Y, Chen L, Zhang XS.

BMC Bioinformatics. 2007 Dec 11;8:475.

12.

Toward prediction of functional protein pockets using blind docking and pocket search algorithms.

Hetényi C, van der Spoel D.

Protein Sci. 2011 May;20(5):880-93. doi: 10.1002/pro.618. Epub 2011 Mar 30.

13.

Mapping of ligand-binding cavities in proteins.

Andersson CD, Chen BY, Linusson A.

Proteins. 2010 May 1;78(6):1408-22. doi: 10.1002/prot.22655. Erratum in: Proteins. 2011 Apr;79(4):1363.

14.

Generalized modeling of enzyme-ligand interactions using proteochemometrics and local protein substructures.

Strömbergsson H, Kryshtafovych A, Prusis P, Fidelis K, Wikberg JE, Komorowski J, Hvidsten TR.

Proteins. 2006 Nov 15;65(3):568-79.

PMID:
16948162
15.

Pocketome via comprehensive identification and classification of ligand binding envelopes.

An J, Totrov M, Abagyan R.

Mol Cell Proteomics. 2005 Jun;4(6):752-61. Epub 2005 Mar 9.

16.

Ligand binding site detection by local structure alignment and its performance complementarity.

Lee HS, Im W.

J Chem Inf Model. 2013 Sep 23;53(9):2462-70. doi: 10.1021/ci4003602. Epub 2013 Sep 4.

17.

BgN-Score and BsN-Score: bagging and boosting based ensemble neural networks scoring functions for accurate binding affinity prediction of protein-ligand complexes.

Ashtawy HM, Mahapatra NR.

BMC Bioinformatics. 2015;16 Suppl 4:S8. doi: 10.1186/1471-2105-16-S4-S8. Epub 2015 Feb 23.

18.

Prediction of ligand binding sites using homologous structures and conservation at CASP8.

Wass MN, Sternberg MJ.

Proteins. 2009;77 Suppl 9:147-51. doi: 10.1002/prot.22513.

19.

Ligand binding site similarity identification based on chemical and geometric similarity.

Tu H, Shi T.

Protein J. 2013 Jun;32(5):373-85. doi: 10.1007/s10930-013-9494-1.

PMID:
23700221
20.

Protein-binding site prediction based on three-dimensional protein modeling.

Oh M, Joo K, Lee J.

Proteins. 2009;77 Suppl 9:152-6. doi: 10.1002/prot.22572.

PMID:
19768678

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