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Results: 1 to 20 of 130

Similar articles for PubMed (Select 23700221)

1.

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
2.

Detecting local ligand-binding site similarity in nonhomologous proteins by surface patch comparison.

Sael L, Kihara D.

Proteins. 2012 Apr;80(4):1177-95. doi: 10.1002/prot.24018. Epub 2012 Jan 24.

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.

PLIC: protein-ligand interaction clusters.

Anand P, Nagarajan D, Mukherjee S, Chandra N.

Database (Oxford). 2014 Apr 23;2014(0):bau029. doi: 10.1093/database/bau029. Print 2014.

5.

Chemogenomics in drug discovery: computational methods based on the comparison of binding sites.

Vulpetti A, Kalliokoski T, Milletti F.

Future Med Chem. 2012 Oct;4(15):1971-9. doi: 10.4155/fmc.12.147. Review.

PMID:
23088277
6.

Constructing patch-based ligand-binding pocket database for predicting function of proteins.

Sael L, Kihara D.

BMC Bioinformatics. 2012 Mar 13;13 Suppl 2:S7. doi: 10.1186/1471-2105-13-S2-S7.

7.

The Poisson Index: a new probabilistic model for protein ligand binding site similarity.

Davies JR, Jackson RM, Mardia KV, Taylor CC.

Bioinformatics. 2007 Nov 15;23(22):3001-8. Epub 2007 Sep 24.

9.

Chemometric analysis of ligand receptor complementarity: identifying Complementary Ligands Based on Receptor Information (CoLiBRI).

Oloff S, Zhang S, Sukumar N, Breneman C, Tropsha A.

J Chem Inf Model. 2006 Mar-Apr;46(2):844-51.

10.

Predicting protein-ligand binding sites based on an improved geometric algorithm.

He J, Wei DQ, Wang JF, Chou KC.

Protein Pept Lett. 2011 Oct;18(10):997-1001.

PMID:
21592081
11.
12.

Protein surface matching by combining local and global geometric information.

Ellingson L, Zhang J.

PLoS One. 2012;7(7):e40540. doi: 10.1371/journal.pone.0040540. Epub 2012 Jul 17.

13.
14.

Ligand-binding site prediction using ligand-interacting and binding site-enriched protein triangles.

Xie ZR, Hwang MJ.

Bioinformatics. 2012 Jun 15;28(12):1579-85. doi: 10.1093/bioinformatics/bts182. Epub 2012 Apr 11.

15.

A global optimization algorithm for protein surface alignment.

Bertolazzi P, Guerra C, Liuzzi G.

BMC Bioinformatics. 2010 Sep 29;11:488. doi: 10.1186/1471-2105-11-488.

16.

FunFOLDQA: a quality assessment tool for protein-ligand binding site residue predictions.

Roche DB, Buenavista MT, McGuffin LJ.

PLoS One. 2012;7(5):e38219. doi: 10.1371/journal.pone.0038219. Epub 2012 May 30.

17.

PESDserv: a server for high-throughput comparison of protein binding site surfaces.

Das S, Krein MP, Breneman CM.

Bioinformatics. 2010 Aug 1;26(15):1913-4. doi: 10.1093/bioinformatics/btq288. Epub 2010 Jun 10.

18.

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.

19.

Assessment of ligand-binding residue predictions in CASP9.

Schmidt T, Haas J, Gallo Cassarino T, Schwede T.

Proteins. 2011;79 Suppl 10:126-36. doi: 10.1002/prot.23174. Epub 2011 Oct 11.

PMID:
21987472
20.

Detection of 3D atomic similarities and their use in the discrimination of small molecule protein-binding sites.

Najmanovich R, Kurbatova N, Thornton J.

Bioinformatics. 2008 Aug 15;24(16):i105-11. doi: 10.1093/bioinformatics/btn263.

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