shaker.umh.es menu
CSS Drop Down Menu by PureCSSMenu.com


Publications → Papers → References

ADAN: A database for prediction of protein-protein interaction of modular domains mediated by linear motifs. J. A. Encinar, Fernandez-Ballester G., Sánchez I.E., Hurtado-Gomez E., Stricher F., Beltrao P., Serrano L. 2009. Bioinformatics. 25(18): 2418-2424.


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