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Items: 1 to 20 of 159

1.

Spatial clustering of protein binding sites for template based protein docking.

Ghoorah AW, Devignes MD, Smaïl-Tabbone M, Ritchie DW.

Bioinformatics. 2011 Oct 15;27(20):2820-7. doi: 10.1093/bioinformatics/btr493. Epub 2011 Aug 27.

PMID:
21873637
2.

KBDOCK 2013: a spatial classification of 3D protein domain family interactions.

Ghoorah AW, Devignes MD, Smaïl-Tabbone M, Ritchie DW.

Nucleic Acids Res. 2014 Jan;42(Database issue):D389-95. doi: 10.1093/nar/gkt1199. Epub 2013 Nov 23.

3.

Protein docking using case-based reasoning.

Ghoorah AW, Devignes MD, Smaïl-Tabbone M, Ritchie DW.

Proteins. 2013 Dec;81(12):2150-8. doi: 10.1002/prot.24433.

PMID:
24123156
4.

3did Update: domain-domain and peptide-mediated interactions of known 3D structure.

Stein A, Panjkovich A, Aloy P.

Nucleic Acids Res. 2009 Jan;37(Database issue):D300-4. doi: 10.1093/nar/gkn690. Epub 2008 Oct 25.

5.

Domain-based small molecule binding site annotation.

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

BMC Bioinformatics. 2006 Mar 17;7:152.

6.

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.

7.

Analysis on multi-domain cooperation for predicting protein-protein interactions.

Wang RS, Wang Y, Wu LY, Zhang XS, Chen L.

BMC Bioinformatics. 2007 Oct 16;8:391.

8.

Predicting domain-domain interaction based on domain profiles with feature selection and support vector machines.

González AJ, Liao L.

BMC Bioinformatics. 2010 Oct 29;11:537. doi: 10.1186/1471-2105-11-537.

9.

PIBASE: a comprehensive database of structurally defined protein interfaces.

Davis FP, Sali A.

Bioinformatics. 2005 May 1;21(9):1901-7. Epub 2005 Jan 18.

PMID:
15657096
10.

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.

11.

Protein-protein interaction site prediction based on conditional random fields.

Li MH, Lin L, Wang XL, Liu T.

Bioinformatics. 2007 Mar 1;23(5):597-604. Epub 2007 Jan 18.

PMID:
17234636
12.

Classification and Exploration of 3D Protein Domain Interactions Using Kbdock.

Ghoorah AW, Devignes MD, Smaïl-Tabbone M, Ritchie DW.

Methods Mol Biol. 2016;1415:91-105. doi: 10.1007/978-1-4939-3572-7_5.

PMID:
27115629
13.

PROTCOM: searchable database of protein complexes enhanced with domain-domain structures.

Kundrotas PJ, Alexov E.

Nucleic Acids Res. 2007 Jan;35(Database issue):D575-9. Epub 2006 Oct 28.

14.

SCOWLP classification: structural comparison and analysis of protein binding regions.

Teyra J, Paszkowski-Rogacz M, Anders G, Pisabarro MT.

BMC Bioinformatics. 2008 Jan 8;9:9. doi: 10.1186/1471-2105-9-9.

15.

3did: a catalog of domain-based interactions of known three-dimensional structure.

Mosca R, Céol A, Stein A, Olivella R, Aloy P.

Nucleic Acids Res. 2014 Jan;42(Database issue):D374-9. doi: 10.1093/nar/gkt887. Epub 2013 Sep 29.

16.

Prediction of Ras-effector interactions using position energy matrices.

Kiel C, Serrano L.

Bioinformatics. 2007 Sep 1;23(17):2226-30. Epub 2007 Jun 28.

PMID:
17599936
17.

Identification of protein interaction partners and protein-protein interaction sites.

Sacquin-Mora S, Carbone A, Lavery R.

J Mol Biol. 2008 Oct 24;382(5):1276-89. doi: 10.1016/j.jmb.2008.08.002. Epub 2008 Aug 7.

PMID:
18708070
18.

Docking and scoring protein interactions: CAPRI 2009.

Lensink MF, Wodak SJ.

Proteins. 2010 Nov 15;78(15):3073-84. doi: 10.1002/prot.22818.

PMID:
20806235
19.

Accounting for conformational changes during protein-protein docking.

Zacharias M.

Curr Opin Struct Biol. 2010 Apr;20(2):180-6. doi: 10.1016/j.sbi.2010.02.001. Epub 2010 Mar 1. Review.

PMID:
20194014
20.

Pushing structural information into the yeast interactome by high-throughput protein docking experiments.

Mosca R, Pons C, Fernández-Recio J, Aloy P.

PLoS Comput Biol. 2009 Aug;5(8):e1000490. doi: 10.1371/journal.pcbi.1000490. Epub 2009 Aug 28.

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