Literature DB >> 24510594

Computational large-scale mapping of protein-protein interactions using structural complexes.

Benjamin Shoemaker1, Stefan Wuchty1, Anna R Panchenko1.   

Abstract

Although the identification of protein interactions by high-throughput methods progresses at a fast pace, "interactome" datasets still suffer from high rates of false positives and low coverage. To map the interactome of any organism, this unit presents a computational framework to predict protein-protein or gene-gene interactions utilizing experimentally determined evidence of structural complexes, atomic details of binding interfaces and evolutionary conservation.
Copyright © 2013 John Wiley & Sons, Inc.

Entities:  

Keywords:  IBIS; Inferred Biomolecular Interactions Server; binding interface; protein interaction; structural complex

Mesh:

Substances:

Year:  2013        PMID: 24510594      PMCID: PMC3920302          DOI: 10.1002/0471140864.ps0309s73

Source DB:  PubMed          Journal:  Curr Protoc Protein Sci        ISSN: 1934-3655


  33 in total

1.  Evolution of protein binding modes in homooligomers.

Authors:  Judith E Dayhoff; Benjamin A Shoemaker; Stephen H Bryant; Anna R Panchenko
Journal:  J Mol Biol       Date:  2009-10-30       Impact factor: 5.469

2.  Predicting protein-protein interactions on a proteome scale by matching evolutionary and structural similarities at interfaces using PRISM.

Authors:  Nurcan Tuncbag; Attila Gursoy; Ruth Nussinov; Ozlem Keskin
Journal:  Nat Protoc       Date:  2011-08-11       Impact factor: 13.491

3.  Struct2Net: a web service to predict protein-protein interactions using a structure-based approach.

Authors:  Rohit Singh; Daniel Park; Jinbo Xu; Raghavendra Hosur; Bonnie Berger
Journal:  Nucleic Acids Res       Date:  2010-05-31       Impact factor: 16.971

4.  CDD: a Conserved Domain Database for the functional annotation of proteins.

Authors:  Aron Marchler-Bauer; Shennan Lu; John B Anderson; Farideh Chitsaz; Myra K Derbyshire; Carol DeWeese-Scott; Jessica H Fong; Lewis Y Geer; Renata C Geer; Noreen R Gonzales; Marc Gwadz; David I Hurwitz; John D Jackson; Zhaoxi Ke; Christopher J Lanczycki; Fu Lu; Gabriele H Marchler; Mikhail Mullokandov; Marina V Omelchenko; Cynthia L Robertson; James S Song; Narmada Thanki; Roxanne A Yamashita; Dachuan Zhang; Naigong Zhang; Chanjuan Zheng; Stephen H Bryant
Journal:  Nucleic Acids Res       Date:  2010-11-24       Impact factor: 16.971

5.  Knowledge-based annotation of small molecule binding sites in proteins.

Authors:  Ratna R Thangudu; Manoj Tyagi; Benjamin A Shoemaker; Stephen H Bryant; Anna R Panchenko; Thomas Madej
Journal:  BMC Bioinformatics       Date:  2010-07-01       Impact factor: 3.169

6.  NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy.

Authors:  Kim D Pruitt; Tatiana Tatusova; Garth R Brown; Donna R Maglott
Journal:  Nucleic Acids Res       Date:  2011-11-24       Impact factor: 16.971

7.  IBIS (Inferred Biomolecular Interaction Server) reports, predicts and integrates multiple types of conserved interactions for proteins.

Authors:  Benjamin A Shoemaker; Dachuan Zhang; Manoj Tyagi; Ratna R Thangudu; Jessica H Fong; Aron Marchler-Bauer; Stephen H Bryant; Thomas Madej; Anna R Panchenko
Journal:  Nucleic Acids Res       Date:  2011-11-18       Impact factor: 16.971

8.  Large-scale mapping of human protein interactome using structural complexes.

Authors:  Manoj Tyagi; Kosuke Hashimoto; Benjamin A Shoemaker; Stefan Wuchty; Anna R Panchenko
Journal:  EMBO Rep       Date:  2012-03-01       Impact factor: 8.807

9.  MMDB: 3D structures and macromolecular interactions.

Authors:  Thomas Madej; Kenneth J Addess; Jessica H Fong; Lewis Y Geer; Renata C Geer; Christopher J Lanczycki; Chunlei Liu; Shennan Lu; Aron Marchler-Bauer; Anna R Panchenko; Jie Chen; Paul A Thiessen; Yanli Wang; Dachuan Zhang; Stephen H Bryant
Journal:  Nucleic Acids Res       Date:  2011-12-01       Impact factor: 16.971

10.  Homology inference of protein-protein interactions via conserved binding sites.

Authors:  Manoj Tyagi; Ratna R Thangudu; Dachuan Zhang; Stephen H Bryant; Thomas Madej; Anna R Panchenko
Journal:  PLoS One       Date:  2012-01-31       Impact factor: 3.240

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