Literature DB >> 23599502

INstruct: a database of high-quality 3D structurally resolved protein interactome networks.

Michael J Meyer1, Jishnu Das, Xiujuan Wang, Haiyuan Yu.   

Abstract

UNLABELLED: INstruct is a database of high-quality, 3D, structurally resolved protein interactome networks in human and six model organisms. INstruct combines the scale of available high-quality binary protein interaction data with the specificity of atomic-resolution structural information derived from co-crystal evidence using a tested interaction interface inference method. Its web interface is designed to allow for flexible search based on standard and organism-specific protein and gene-naming conventions, visualization of protein architecture highlighting interaction interfaces and viewing and downloading custom 3D structurally resolved interactome datasets. AVAILABILITY: INstruct is freely available on the web at http://instruct.yulab.org with all major browsers supported.

Entities:  

Mesh：

Year:  2013        PMID： 23599502      PMCID： PMC3673217          DOI： 10.1093/bioinformatics/btt181

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  24 in total

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Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

Review 2.  Protein-protein interactions define specificity in signal transduction.

Authors:  T Pawson; P Nash
Journal:  Genes Dev       Date:  2000-05-01       Impact factor: 11.361

3.  The Database of Interacting Proteins: 2004 update.

Authors:  Lukasz Salwinski; Christopher S Miller; Adam J Smith; Frank K Pettit; James U Bowie; David Eisenberg
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

4.  iPfam: visualization of protein-protein interactions in PDB at domain and amino acid resolutions.

Authors:  Robert D Finn; Mhairi Marshall; Alex Bateman
Journal:  Bioinformatics       Date:  2004-09-07       Impact factor: 6.937

Review 5.  Network medicine: a network-based approach to human disease.

Authors:  Albert-László Barabási; Natali Gulbahce; Joseph Loscalzo
Journal:  Nat Rev Genet       Date:  2011-01       Impact factor: 53.242

6.  iRefWeb: interactive analysis of consolidated protein interaction data and their supporting evidence.

Authors:  Brian Turner; Sabry Razick; Andrei L Turinsky; James Vlasblom; Edgard K Crowdy; Emerson Cho; Kyle Morrison; Ian M Donaldson; Shoshana J Wodak
Journal:  Database (Oxford)       Date:  2010-10-12       Impact factor: 3.451

7.  Ongoing and future developments at the Universal Protein Resource.

Authors: 
Journal:  Nucleic Acids Res       Date:  2010-11-04       Impact factor: 16.971

8.  The BioGRID Interaction Database: 2011 update.

Authors:  Chris Stark; Bobby-Joe Breitkreutz; Andrew Chatr-Aryamontri; Lorrie Boucher; Rose Oughtred; Michael S Livstone; Julie Nixon; Kimberly Van Auken; Xiaodong Wang; Xiaoqi Shi; Teresa Reguly; Jennifer M Rust; Andrew Winter; Kara Dolinski; Mike Tyers
Journal:  Nucleic Acids Res       Date:  2010-11-11       Impact factor: 16.971

9.  MIPS: curated databases and comprehensive secondary data resources in 2010.

Authors:  H Werner Mewes; Andreas Ruepp; Fabian Theis; Thomas Rattei; Mathias Walter; Dmitrij Frishman; Karsten Suhre; Manuel Spannagl; Klaus F X Mayer; Volker Stümpflen; Alexey Antonov
Journal:  Nucleic Acids Res       Date:  2010-11-24       Impact factor: 16.971

10.  Protein interactions in human genetic diseases.

Authors:  Benjamin Schuster-Böckler; Alex Bateman
Journal:  Genome Biol       Date:  2008-01-16       Impact factor: 13.583
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  60 in total

1.  Dissecting disease inheritance modes in a three-dimensional protein network challenges the "guilt-by-association" principle.

Authors:  Yu Guo; Xiaomu Wei; Jishnu Das; Andrew Grimson; Steven M Lipkin; Andrew G Clark; Haiyuan Yu
Journal:  Am J Hum Genet       Date:  2013-06-20       Impact factor: 11.025

2.  Extending RosettaDock with water, sugar, and pH for prediction of complex structures and affinities for CAPRI rounds 20-27.

Authors:  Krishna Praneeth Kilambi; Michael S Pacella; Jianqing Xu; Jason W Labonte; Justin R Porter; Pravin Muthu; Kevin Drew; Daisuke Kuroda; Ora Schueler-Furman; Richard Bonneau; Jeffrey J Gray
Journal:  Proteins       Date:  2013-10-17

3.  A Systems Pharmacology Approach Uncovers Wogonoside as an Angiogenesis Inhibitor of Triple-Negative Breast Cancer by Targeting Hedgehog Signaling.

Authors:  Yujie Huang; Jiansong Fang; Weiqiang Lu; Zihao Wang; Qi Wang; Yuan Hou; Xingwu Jiang; Ofer Reizes; Justin Lathia; Ruth Nussinov; Charis Eng; Feixiong Cheng
Journal:  Cell Chem Biol       Date:  2019-06-06       Impact factor: 8.116

4.  mPPI: a database extension to visualize structural interactome in a one-to-many manner.

Authors:  Yekai Zhou; Hongjun Chen; Sida Li; Ming Chen
Journal:  Database (Oxford)       Date:  2021-06-22       Impact factor: 3.451

Review 5.  Molecular networks in Network Medicine: Development and applications.

Authors:  Edwin K Silverman; Harald H H W Schmidt; Eleni Anastasiadou; Lucia Altucci; Marco Angelini; Lina Badimon; Jean-Luc Balligand; Giuditta Benincasa; Giovambattista Capasso; Federica Conte; Antonella Di Costanzo; Lorenzo Farina; Giulia Fiscon; Laurent Gatto; Michele Gentili; Joseph Loscalzo; Cinzia Marchese; Claudio Napoli; Paola Paci; Manuela Petti; John Quackenbush; Paolo Tieri; Davide Viggiano; Gemma Vilahur; Kimberly Glass; Jan Baumbach
Journal:  Wiley Interdiscip Rev Syst Biol Med       Date:  2020-04-19

Review 6.  Exploring mechanisms of human disease through structurally resolved protein interactome networks.

Authors:  Robert Fragoza; Hao Ran Lee; Nicolas A Cordero; Jishnu Das; Yu Guo; Michael J Meyer; Tommy V Vo; Xiujuan Wang; Haiyuan Yu
Journal:  Mol Biosyst       Date:  2014-01

Review 7.  Genotype to phenotype via network analysis.

Authors:  Hannah Carter; Matan Hofree; Trey Ideker
Journal:  Curr Opin Genet Dev       Date:  2013-11-14       Impact factor: 5.578

8.  A network medicine approach to investigation and population-based validation of disease manifestations and drug repurposing for COVID-19.

Authors:  Yadi Zhou; Yuan Hou; Jiayu Shen; Reena Mehra; Asha Kallianpur; Daniel A Culver; Michaela U Gack; Samar Farha; Joe Zein; Suzy Comhair; Claudio Fiocchi; Thaddeus Stappenbeck; Timothy Chan; Charis Eng; Jae U Jung; Lara Jehi; Serpil Erzurum; Feixiong Cheng
Journal:  PLoS Biol       Date:  2020-11-06       Impact factor: 8.029

Review 9.  Advances in computational approaches for prioritizing driver mutations and significantly mutated genes in cancer genomes.

Authors:  Feixiong Cheng; Junfei Zhao; Zhongming Zhao
Journal:  Brief Bioinform       Date:  2015-08-24       Impact factor: 11.622

Review 10.  Structural bioinformatics of the interactome.

Authors:  Donald Petrey; Barry Honig
Journal:  Annu Rev Biophys       Date:  2014       Impact factor: 12.981
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