SCOPPI: a structural classification of protein–protein interfaces

SCOPPI, the structural classification of protein–protein interfaces, is a comprehensive database that classifies and annotates domain interactions derived from all known protein structures. SCOPPI applies SCOP domain definitions and a distance criterion to determine inter-domain interfaces. Using a novel method based on multiple sequence and structural alignments of SCOP families, SCOPPI presents a comprehensive geometrical classification of domain interfaces. Various interface characteristics such as number, type and position of interacting amino acids, conservation, interface size, and permanent or transient nature of the interaction are further provided. Proteins in SCOPPI are annotated with Gene Ontology terms, and the ontology can be used to quickly browse SCOPPI. Screenshots are available for every interface and its participating domains. Here, we describe contents and features of the web-based user interface as well as the underlying methods used to generate SCOPPI's data. In addition, we present a number of examples where SCOPPI becomes a useful tool to analyze viral mimicry of human interface binding sites, gene fusion events, conservation of interface residues and diversity of interface localizations. SCOPPI is available at .

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

[2]  Tim J. P. Hubbard,et al.  SCOP database in 2004: refinements integrate structure and sequence family data , 2004, Nucleic Acids Res..

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

[4]  Robert B. Russell,et al.  InterPreTS: protein Interaction Prediction through Tertiary Structure , 2003, Bioinform..

[5]  Cathy H. Wu,et al.  InterPro, progress and status in 2005 , 2004, Nucleic Acids Res..

[6]  S. L. Wong,et al.  A Map of the Interactome Network of the Metazoan C. elegans , 2004, Science.

[7]  Jon C Ison,et al.  Survey of the geometric association of domain–domain interfaces , 2005, Proteins.

[8]  H. Wolfson,et al.  A dataset of protein-protein interfaces generated with a sequence-order-independent comparison technique. , 1996, Journal of molecular biology.

[9]  J. Thornton,et al.  PQS: a protein quaternary structure file server. , 1998, Trends in biochemical sciences.

[10]  James R. Knight,et al.  A Protein Interaction Map of Drosophila melanogaster , 2003, Science.

[11]  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.

[12]  Dan M. Bolser,et al.  Using convex hulls to extract interaction interfaces from known structures , 2004, Bioinform..

[13]  Kyungsook Han,et al.  PSIbase: a database of Protein Structural Interactome map (PSIMAP) , 2005, Bioinform..

[14]  Emily Dimmer,et al.  The Gene Ontology Annotation (GOA) Database - An integrated resource of GO annotations to the UniProt Knowledgebase , 2003, Silico Biol..

[15]  Gene Ontology Consortium.  The Gene Ontology (GO) database and informatics resource , 2003 .

[16]  Michael Schroeder,et al.  GoPubMed: exploring PubMed with the Gene Ontology , 2005, Nucleic Acids Res..

[17]  B. Lee,et al.  The interpretation of protein structures: estimation of static accessibility. , 1971, Journal of molecular biology.

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

[19]  Martin Vingron,et al.  IntAct: an open source molecular interaction database , 2004, Nucleic Acids Res..

[20]  P. Argos,et al.  Cavities and packing at protein interfaces , 1994, Protein science : a publication of the Protein Society.

[21]  J. Wojcik,et al.  The protein–protein interaction map of Helicobacter pylori , 2001, Nature.

[22]  Adam Godzik,et al.  Clustering of highly homologous sequences to reduce the size of large protein databases , 2001, Bioinform..

[23]  Christian von Mering,et al.  STRING: known and predicted protein–protein associations, integrated and transferred across organisms , 2004, Nucleic Acids Res..

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

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

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

[27]  Sarah A. Teichmann,et al.  Principles of protein-protein interactions , 2002, ECCB.

[28]  Tracy M. Handel,et al.  Structural Basis of Chemokine Sequestration by a Herpesvirus Decoy Receptor , 2002, Cell.

[29]  R. Raz,et al.  ProMate: a structure based prediction program to identify the location of protein-protein binding sites. , 2004, Journal of molecular biology.

[30]  Ruth Nussinov,et al.  A method for simultaneous alignment of multiple protein structures , 2004, Proteins.

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

[32]  Luhua Lai,et al.  Structure-based method for analyzing protein–protein interfaces , 2004, Journal of molecular modeling.

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

[34]  Robert C. Edgar,et al.  MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.

[35]  J. Matthews,et al.  Protein-protein interactions in human disease. , 2005, Current opinion in structural biology.

[36]  Jong H. Park,et al.  Mapping protein family interactions: intramolecular and intermolecular protein family interaction repertoires in the PDB and yeast. , 2001, Journal of molecular biology.

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

[38]  V Jo Davisson,et al.  Toward understanding the mechanism of the complex cyclization reaction catalyzed by imidazole glycerolphosphate synthase: crystal structures of a ternary complex and the free enzyme. , 2003, Biochemistry.