ADAN: A database for prediction of protein-protein interaction of modular domains mediated by linear motifs

Bioinformatics

Volumn 25, Issue 18, 2009, Pages 2418-2424

  Encinar, J A ^a   Fernandez Ballester, Gregorio ^a   Sanchez I E ^b   Hurtado Gomez, E ^a,c   Stricher, F ^c   Beltrao, P ^d   Serrano, L ^c  

^a MIGUEL HERNÁNDEZ UNIVERSITY   (Spain)

^b FUNDACIÓN INSTITUTO LELOIR   (Argentina)

^c CENTRE FOR GENOMIC REGULATION CRG   (Spain)

^d UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PDZ PROTEIN; PROTEIN SH2; PROTEIN SH3;

ACCESS TO INFORMATION; AMINO ACID SEQUENCE; ARTICLE; BIOCHEMISTRY; INFORMATION PROCESSING; INTERNET; ONLINE SYSTEM; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN DATABASE; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN MOTIF; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; SEQUENCE ALIGNMENT; THERMODYNAMICS;

ALGORITHMS; AMINO ACID MOTIFS; BINDING SITES; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; PROTEIN INTERACTION MAPPING; PROTEIN STRUCTURE, TERTIARY; PROTEINS; SEQUENCE ANALYSIS, PROTEIN; SOFTWARE;

EID: 69849100180     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btp424     Document Type: Article

References (37)

1. Aloy,P. and Russell,R.B. (2002) Interrogating protein interaction networks through structural biology. Proc. Natl Acad. Sci. USA, 99, 5896-5901.
2. Apweiler,R. et al. (2001) The InterPro database, an integrated documentation resource for protein families, domains and functional sites. Nucleic Acids Res., 29, 37-40.
3. Bairoch,A. et al. (2005) The universal protein resource (UniProt). Nucleic Acids Res., 33, D154-D159.
4. Berman,H. et al. (2003) Announcing the worldwide Protein Data Bank. Nat. Struct. Biol., 10, 980.
5. Ceol,A. et al. (2007) DOMINO: A database of domain-peptide interactions. Nucleic Acids Res., 35, D557-D560.
6. Chatr-aryamontri,A. et al. (2007) MINT: The Molecular INTeraction database. Nucleic Acids Res., 35, D572-D574.
7. Fernandez-Ballester,G. and Serrano,L. (2006) Prediction of protein-protein interaction based on structure. Methods Mol. Biol. 340, 207-234.
8. Fernandez-Ballester,G. et al. (2009) Structure-based prediction of the Saccharomyces cerevisiae SH3-ligand interactions. J. Mol. Biol., 388, 902-916.
9. Fernandez-Ballester,G. et al. (2004) The tryptophan switch: changing ligand-binding specificity from type I to type II in SH3 domains. J. Mol. Biol., 335, 619-629.
10. Finn,R.D. et al. (2005) iPfam: Visualization of protein-protein interactions in PDB at domain and amino acid resolutions. Bioinformatics, 21, 410-412.
11. Finn,R.D. et al. (2006) Pfam: Clans, web tools and services. Nucleic Acids Res., 34, D247-D251.
12. Gasteiger,E. et al. (2001) SWISS-PROT: Connecting biomolecular knowledge via a protein database. Curr. Issues Mol. Biol., 3 47-55.
13. Gavin,A.C. et al. (2006) Proteome survey reveals modularity of the yeast cell machinery. Nature, 440, 631-636.
14. Gong,S. et al. (2005a) A protein domain interaction interface database: InterPare. BMC. Bioinformatics, 6, 207.
15. Gong,S. et al. (2005b) PSIbase: A database of protein structural interactome map (PSIMAP). Bioinformatics, 21, 2541-2543.
16. Guerois,R. et al. (2002) Predicting changes in the stability of proteins and protein complexes: A study of more than 1000 mutations. J. Mol. Biol., 320, 369-387.
17. Kempkens,O. et al. (2006) Computer modelling in combination with in vitro studies reveals similar binding affinities of Drosophila Crumbs for the PDZ domains of Stardust and DmPar-6. Eur. J. Cell Biol., 85, 753-767.
18. Kiel,C. and Serrano,L. (2006) The ubiquitin domain superfold: structure-based sequence alignments and characterization of binding epitopes. J. Mol. Biol., 355, 821-844.
19. Kiel,C. et al. (2004) A detailed thermodynamic analysis of ras/ effector complex interfaces. J. Mol. Biol., 340, 1039-1058.
20. Kiel,C. et al. (2005) Recognizing and defining true Ras binding domains II: In silico prediction based on homology modelling and energy calculations. J. Mol. Biol., 348, 759-75.
21. Kolsch,V. et al. (2007) Control of Drosophila gastrulation by apical localization of adherens junctions and RhoGEF2. Science, 315, 384-386.
22. Laskowski,R.A. et al. (2005) PDBsum more: New summaries and analyses of the known 3D structures of proteins and nucleic acids. Nucleic Acids Res., 33, D266-D268.
23. Letunic,I. et al. (2006) SMART 5: Domains in the context of genomes and networks. Nucleic Acids Res., 34, D257-D260.
24. Linding,R. et al. (2003) GlobPlot: Exploring protein sequences for globularity and disorder. Nucleic Acids Res., 31, 3701-3708.
25. Marti-Renom,M.A. et al. (2000) Comparative protein structure modeling of genes and genomes. Annu. Rev. Biophys. Biomol. Struct. 29, 291-325.
26. Milburn,D. et al. (1998) Sequences annotated by structure: A tool to facilitate the use of structural information in sequence analysis. Protein Eng., 11, 855-859.
27. Mulder,N.J. et al. (2005) InterPro, progress and status in 2005. Nucleic Acids Res., 33, D201-D205.
28. Ogmen,U. et al. (2005) PRISM: Protein interactions by structural matching. Nucleic Acids Res., 33, W331-W336.
29. Pieper,U. et al. (2006) MODBASE: A database of annotated comparative protein structure models and associated resources. Nucleic Acids Res., 34, D291-D295.
30. Ponting,C.P. et al. (1999) SMART: Identification and annotation of domains from signalling and extracellular protein sequences. Nucleic Acids Res., 27, 229-232.
31. Prieto,C. and de las Rivas,J. (2006) APID: Agile protein interaction DataAnalyzer. Nucleic Acids Res., 34, W298-W302.
32. Sanchez,I.E. et al. (2008) Genome-wide prediction of SH2 domain targets using structural information and the FoldX algorithm. PLoS Comput. Biol., 4, e1000052.
33. Schultz,J. et al. (1998) SMART, a simple modular architecture research tool: Identification of signaling domains. Proc. Natl. Acad. Sci. U S A, 95, 5857-5864.
34. Schymkowitz,J. et al. (2005) The FoldX web server: An online force field. Nucleic Acids Res., 33, W382-W388.
35. Tagari,M. et al. (2006) E-MSD: Improving data deposition and structure quality. Nucleic Acids Res., 34, D287-D290.
36. Villanueva,J. et al. (2003) Ligand screening by exoproteolysis and mass spectrometry in combination with computer modelling. J. Mol. Biol., 330, 1039-1048.
37. Wallace,A.C. et al. (1995) LIGPLOT: A program to generate schematic diagrams of protein-ligand interactions. Protein Eng., 8, 127-134.