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Results: 1 to 20 of 167

1.

Predicting where small molecules bind at protein-protein interfaces.

Walter P, Metzger J, Thiel C, Helms V.

PLoS One. 2013;8(3):e58583. doi: 10.1371/journal.pone.0058583. Epub 2013 Mar 7.

PMID:
23505538
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Blind predictions of protein interfaces by docking calculations in CAPRI.

Lensink MF, Wodak SJ.

Proteins. 2010 Nov 15;78(15):3085-95. doi: 10.1002/prot.22850.

PMID:
20839234
[PubMed - indexed for MEDLINE]
3.

The distribution of ligand-binding pockets around protein-protein interfaces suggests a general mechanism for pocket formation.

Gao M, Skolnick J.

Proc Natl Acad Sci U S A. 2012 Mar 6;109(10):3784-9. doi: 10.1073/pnas.1117768109. Epub 2012 Feb 21.

PMID:
22355140
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Domain-based small molecule binding site annotation.

Snyder KA, Feldman HJ, Dumontier M, Salama JJ, Hogue CW.

BMC Bioinformatics. 2006 Mar 17;7:152.

PMID:
16545112
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Conserved residue clusters at protein-protein interfaces and their use in binding site identification.

Guharoy M, Chakrabarti P.

BMC Bioinformatics. 2010 May 27;11:286. doi: 10.1186/1471-2105-11-286.

PMID:
20507585
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Protein-protein alternative binding modes do not overlap.

Kundrotas PJ, Vakser IA.

Protein Sci. 2013 Aug;22(8):1141-5. doi: 10.1002/pro.2295. Epub 2013 Jul 3.

PMID:
23775945
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Comprehensive identification of "druggable" protein ligand binding sites.

An J, Totrov M, Abagyan R.

Genome Inform. 2004;15(2):31-41.

PMID:
15706489
[PubMed - indexed for MEDLINE]
8.

Structural and functional characterization of binding sites in metallocarboxypeptidases based on Optimal Docking Area analysis.

Fernández D, Vendrell J, Avilés FX, Fernández-Recio J.

Proteins. 2007 Jul 1;68(1):131-44.

PMID:
17407161
[PubMed - indexed for MEDLINE]
9.

Characterization and prediction of protein interfaces to infer protein-protein interaction networks.

Keskin O, Tuncbag N, Gursoy A.

Curr Pharm Biotechnol. 2008 Apr;9(2):67-76. Review.

PMID:
18393863
[PubMed - indexed for MEDLINE]
10.

Statistical analysis and prediction of protein-protein interfaces.

Bordner AJ, Abagyan R.

Proteins. 2005 Aug 15;60(3):353-66.

PMID:
15906321
[PubMed - indexed for MEDLINE]
11.

SCOWLP: a web-based database for detailed characterization and visualization of protein interfaces.

Teyra J, Doms A, Schroeder M, Pisabarro MT.

BMC Bioinformatics. 2006 Mar 2;7:104.

PMID:
16512892
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Computational prediction of protein-protein complexes.

Mishra S.

BMC Res Notes. 2012 Sep 9;5:495. doi: 10.1186/1756-0500-5-495.

PMID:
22958278
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Visualisation of variable binding pockets on protein surfaces by probabilistic analysis of related structure sets.

Ashford P, Moss DS, Alex A, Yeap SK, Povia A, Nobeli I, Williams MA.

BMC Bioinformatics. 2012 Mar 14;13:39. doi: 10.1186/1471-2105-13-39.

PMID:
22417279
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Accuracy of protein-protein binding sites in high-throughput template-based modeling.

Kundrotas PJ, Vakser IA.

PLoS Comput Biol. 2010 Apr 1;6(4):e1000727. doi: 10.1371/journal.pcbi.1000727.

PMID:
20369011
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

How proteins get in touch: interface prediction in the study of biomolecular complexes.

de Vries SJ, Bonvin AM.

Curr Protein Pept Sci. 2008 Aug;9(4):394-406.

PMID:
18691126
[PubMed - indexed for MEDLINE]
16.

Joint evolutionary trees: a large-scale method to predict protein interfaces based on sequence sampling.

Engelen S, Trojan LA, Sacquin-Mora S, Lavery R, Carbone A.

PLoS Comput Biol. 2009 Jan;5(1):e1000267. doi: 10.1371/journal.pcbi.1000267. Epub 2009 Jan 23.

PMID:
19165315
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Comprehensive inventory of protein complexes in the Protein Data Bank from consistent classification of interfaces.

Bordner AJ, Gorin AA.

BMC Bioinformatics. 2008 May 12;9:234. doi: 10.1186/1471-2105-9-234.

PMID:
18474114
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Preparation and refinement of model protein-ligand complexes.

Orry AJ, Abagyan R.

Methods Mol Biol. 2012;857:351-73. doi: 10.1007/978-1-61779-588-6_16.

PMID:
22323230
[PubMed - indexed for MEDLINE]
19.

PRISM: protein-protein interaction prediction by structural matching.

Keskin O, Nussinov R, Gursoy A.

Methods Mol Biol. 2008;484:505-21. doi: 10.1007/978-1-59745-398-1_30.

PMID:
18592198
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Analysis of hot region organization in hub proteins.

Cukuroglu E, Gursoy A, Keskin O.

Ann Biomed Eng. 2010 Jun;38(6):2068-78. doi: 10.1007/s10439-010-0048-9. Epub 2010 May 1.

PMID:
20437205
[PubMed - indexed for MEDLINE]

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