PiSite: a database of protein interaction sites using multiple binding states in the PDB

The vast accumulation of protein structural data has now facilitated the observation of many different complexes in the PDB for the same protein. Therefore, a single protein complex is not sufficient to identify their interaction sites, especially for proteins with multiple binding states or different partners, such as hub proteins. PiSite is a database that provides protein–protein interaction sites at the residue level with consideration of multiple complexes at the same time, by mapping the binding sites of all complexes containing the same protein in the PDB. PiSite provides easy web interfaces with an interactive viewer working with typical web browsers, and the different binding modes can be checked visually. All of the information can also be downloaded for further analyses. In addition, PiSite provides a list of proteins with multiple binding partners and multiple binding states, as well as up-to-date statistics of protein–protein interfaces. PiSite is available at http://pisite.hgc.jp

[1]  E. Scolnick,et al.  Identification of effector residues and a neutralizing epitope of Ha-ras-encoded p21. , 1986, Proceedings of the National Academy of Sciences of the United States of America.

[2]  A. Barabasi,et al.  Lethality and centrality in protein networks , 2001, Nature.

[3]  J. Thornton,et al.  Protein–protein interfaces: Analysis of amino acid conservation in homodimers , 2001, Proteins.

[4]  Gary D Bader,et al.  Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry , 2002, Nature.

[5]  S. Teichmann,et al.  Assembly reflects evolution of protein complexes , 2008, Nature.

[6]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[7]  James R. Knight,et al.  A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae , 2000, Nature.

[8]  Steven E Brenner,et al.  The Impact of Structural Genomics: Expectations and Outcomes , 2005, Science.

[9]  Thomas L. Madden,et al.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.

[10]  P. Bork,et al.  Functional organization of the yeast proteome by systematic analysis of protein complexes , 2002, Nature.

[11]  Robert D. Finn,et al.  iPfam: visualization of protein?Cprotein interactions in PDB at domain and amino acid resolutions , 2005, Bioinform..

[12]  J M Thornton,et al.  Protein-protein interactions: a review of protein dimer structures. , 1995, Progress in biophysics and molecular biology.

[13]  Michael Schroeder,et al.  SCOPPI: a structural classification of protein–protein interfaces , 2005, Nucleic Acids Res..

[14]  R. Nussinov,et al.  Principles of protein-protein interactions: what are the preferred ways for proteins to interact? , 2008, Chemical reviews.

[15]  Robert B. Russell,et al.  3did: interacting protein domains of known three-dimensional structure , 2004, Nucleic Acids Res..

[16]  M. Kimmel,et al.  Conflict of interest statement. None declared. , 2010 .

[17]  Sarah A. Teichmann,et al.  3D Complex: A Structural Classification of Protein Complexes , 2006, PLoS Comput. Biol..

[18]  Motonori Ota,et al.  Protein structural change upon ligand binding correlates with enzymatic reaction mechanism. , 2008, Journal of molecular biology.

[19]  Teresa M. Przytycka,et al.  DOMINE: a database of protein domain interactions , 2007, Nucleic Acids Res..

[20]  Huan-Xiang Zhou,et al.  Interaction-site prediction for protein complexes: a critical assessment , 2007, Bioinform..

[21]  R. Ozawa,et al.  A comprehensive two-hybrid analysis to explore the yeast protein interactome , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[22]  Fred P. Davis,et al.  PIBASE: a comprehensive database of structurally defined protein interfaces , 2005, Bioinform..

[23]  M. Schroeder,et al.  Using protein binding site prediction to improve protein docking. , 2008, Gene.

[24]  J. Janin,et al.  A dissection of specific and non-specific protein-protein interfaces. , 2004, Journal of molecular biology.

[25]  Kengo Kinoshita,et al.  eF-site and PDBjViewer: database and viewer for protein functional sites , 2004, Bioinform..

[26]  Dan M. Bolser,et al.  Large-scale co-evolution analysis of protein structural interlogues using the global protein structural interactome map (PSIMAP) , 2004, Bioinform..

[27]  Kengo Kinoshita,et al.  Identification of transient hub proteins and the possible structural basis for their multiple interactions , 2008, Protein science : a publication of the Protein Society.