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Results: 1 to 20 of 109

Similar articles for PubMed (Select 24271397)

1.

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.

2.

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.

3.

iPfam: a database of protein family and domain interactions found in the Protein Data Bank.

Finn RD, Miller BL, Clements J, Bateman A.

Nucleic Acids Res. 2014 Jan;42(Database issue):D364-73. doi: 10.1093/nar/gkt1210. Epub 2013 Dec 1.

4.

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.

5.

A structure-based classification and analysis of protein domain family binding sites and their interactions.

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

Biology (Basel). 2015 Apr 9;4(2):327-43. doi: 10.3390/biology4020327.

6.

Domain-based small molecule binding site annotation.

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

BMC Bioinformatics. 2006 Mar 17;7:152.

7.

PSIbase: a database of Protein Structural Interactome map (PSIMAP).

Gong S, Yoon G, Jang I, Bolser D, Dafas P, Schroeder M, Choi H, Cho Y, Han K, Lee S, Choi H, Lappe M, Holm L, Kim S, Oh D, Bhak J.

Bioinformatics. 2005 May 15;21(10):2541-3. Epub 2005 Mar 3.

8.

The PAS fold. A redefinition of the PAS domain based upon structural prediction.

Hefti MH, Françoijs KJ, de Vries SC, Dixon R, Vervoort J.

Eur J Biochem. 2004 Mar;271(6):1198-208.

PMID:
15009198
9.

The protein common interface database (ProtCID)--a comprehensive database of interactions of homologous proteins in multiple crystal forms.

Xu Q, Dunbrack RL Jr.

Nucleic Acids Res. 2011 Jan;39(Database issue):D761-70. doi: 10.1093/nar/gkq1059. Epub 2010 Oct 29.

10.

Assignment of protein sequences to existing domain and family classification systems: Pfam and the PDB.

Xu Q, Dunbrack RL Jr.

Bioinformatics. 2012 Nov 1;28(21):2763-72. doi: 10.1093/bioinformatics/bts533. Epub 2012 Aug 31.

11.

Discovering interacting domains and motifs in protein-protein interactions.

Hugo W, Sung WK, Ng SK.

Methods Mol Biol. 2013;939:9-20. doi: 10.1007/978-1-62703-107-3_2.

PMID:
23192537
12.

3D-interologs: an evolution database of physical protein- protein interactions across multiple genomes.

Lo YS, Chen YC, Yang JM.

BMC Genomics. 2010 Dec 1;11 Suppl 3:S7. doi: 10.1186/1471-2164-11-S3-S7.

13.

DAPID: a 3D-domain annotated protein-protein interaction database.

Chen YC, Chen HC, Yang JM.

Genome Inform. 2006;17(2):206-15.

PMID:
17503393
14.

The Pfam protein families database.

Bateman A, Birney E, Cerruti L, Durbin R, Etwiller L, Eddy SR, Griffiths-Jones S, Howe KL, Marshall M, Sonnhammer EL.

Nucleic Acids Res. 2002 Jan 1;30(1):276-80.

15.

The ProDom database of protein domain families: more emphasis on 3D.

Bru C, Courcelle E, Carrère S, Beausse Y, Dalmar S, Kahn D.

Nucleic Acids Res. 2005 Jan 1;33(Database issue):D212-5.

16.

The Pfam protein families database.

Finn RD, Tate J, Mistry J, Coggill PC, Sammut SJ, Hotz HR, Ceric G, Forslund K, Eddy SR, Sonnhammer EL, Bateman A.

Nucleic Acids Res. 2008 Jan;36(Database issue):D281-8. Epub 2007 Nov 26.

17.

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
18.

Reconstituting protein interaction networks using parameter-dependent domain-domain interactions.

Memišević V, Wallqvist A, Reifman J.

BMC Bioinformatics. 2013 May 7;14:154. doi: 10.1186/1471-2105-14-154.

19.

Search similar protein structures with classification, sequence and 3d alignments.

Lu Z, Zhao Z, Garcia S, Krishnaswamy K, Fu B.

J Bioinform Comput Biol. 2009 Oct;7(5):755-71.

PMID:
19785044
20.

DOMINE: a database of protein domain interactions.

Raghavachari B, Tasneem A, Przytycka TM, Jothi R.

Nucleic Acids Res. 2008 Jan;36(Database issue):D656-61. Epub 2007 Oct 2.

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