Literature DB >> 20525940

Computational tools for the interactive exploration of proteomic and structural data.

John H Morris1, Elaine C Meng, Thomas E Ferrin.   

Abstract

Linking proteomics and structural data is critical to our understanding of cellular processes, and interactive exploration of these complementary data sets can be extremely valuable for developing or confirming hypotheses in silico. However, few computational tools facilitate linking these types of data interactively. In addition, the tools that do exist are neither well understood nor widely used by the proteomics or structural biology communities. We briefly describe several relevant tools, and then, using three scenarios, we present in depth two tools for the integrated exploration of proteomics and structural data.

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Year:  2010        PMID: 20525940      PMCID: PMC2938059          DOI: 10.1074/mcp.R000007-MCP201

Source DB:  PubMed          Journal:  Mol Cell Proteomics        ISSN: 1535-9476            Impact factor:   5.911


  73 in total

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

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Authors:  H M Berman; J Westbrook; Z Feng; G Gilliland; T N Bhat; H Weissig; I N Shindyalov; P E Bourne
Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

3.  Integration of biological networks and gene expression data using Cytoscape.

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Journal:  Nat Protoc       Date:  2007       Impact factor: 13.491

4.  Cluster analysis and display of genome-wide expression patterns.

Authors:  M B Eisen; P T Spellman; P O Brown; D Botstein
Journal:  Proc Natl Acad Sci U S A       Date:  1998-12-08       Impact factor: 11.205

5.  Human Protein Reference Database and Human Proteinpedia as discovery tools for systems biology.

Authors:  T S Keshava Prasad; Kumaran Kandasamy; Akhilesh Pandey
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6.  Human intestinal H+/peptide cotransporter. Cloning, functional expression, and chromosomal localization.

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Journal:  J Biol Chem       Date:  1995-03-24       Impact factor: 5.157

7.  Structures of human cytosolic NADP-dependent isocitrate dehydrogenase reveal a novel self-regulatory mechanism of activity.

Authors:  Xiang Xu; Jingyue Zhao; Zhen Xu; Baozhen Peng; Qiuhua Huang; Eddy Arnold; Jianping Ding
Journal:  J Biol Chem       Date:  2004-06-01       Impact factor: 5.157

8.  Molecular cloning of the human kidney differentiation antigen gp160: human aminopeptidase A.

Authors:  D M Nanus; D Engelstein; G A Gastl; L Gluck; M J Vidal; M Morrison; C L Finstad; N H Bander; A P Albino
Journal:  Proc Natl Acad Sci U S A       Date:  1993-08-01       Impact factor: 11.205

9.  Reactome knowledgebase of human biological pathways and processes.

Authors:  Lisa Matthews; Gopal Gopinath; Marc Gillespie; Michael Caudy; David Croft; Bernard de Bono; Phani Garapati; Jill Hemish; Henning Hermjakob; Bijay Jassal; Alex Kanapin; Suzanna Lewis; Shahana Mahajan; Bruce May; Esther Schmidt; Imre Vastrik; Guanming Wu; Ewan Birney; Lincoln Stein; Peter D'Eustachio
Journal:  Nucleic Acids Res       Date:  2008-11-03       Impact factor: 16.971

10.  PID: the Pathway Interaction Database.

Authors:  Carl F Schaefer; Kira Anthony; Shiva Krupa; Jeffrey Buchoff; Matthew Day; Timo Hannay; Kenneth H Buetow
Journal:  Nucleic Acids Res       Date:  2008-10-02       Impact factor: 16.971

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  5 in total

1.  Topological analysis and interactive visualization of biological networks and protein structures.

Authors:  Nadezhda T Doncheva; Yassen Assenov; Francisco S Domingues; Mario Albrecht
Journal:  Nat Protoc       Date:  2012-03-15       Impact factor: 13.491

2.  Interactive JIMD articles using the iSee concept: turning a new page on structural biology data.

Authors:  Wen Hwa Lee; Wyatt W Yue; Eugene Raush; Maxim Totrov; Ruben Abagyan; Udo Oppermann; Brian D Marsden
Journal:  J Inherit Metab Dis       Date:  2011-04-21       Impact factor: 4.982

Review 3.  Structural bioinformatics of the interactome.

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

4.  Allosteric signalling in the outer membrane translocation domain of PapC usher.

Authors:  Irene Farabella; Thieng Pham; Nadine S Henderson; Sebastian Geibel; Gilles Phan; David G Thanassi; Anne H Delcour; Gabriel Waksman; Maya Topf
Journal:  Elife       Date:  2014-10-28       Impact factor: 8.140

5.  Ten simple rules to create biological network figures for communication.

Authors:  G Elisabeta Marai; Bruno Pinaud; Katja Bühler; Alexander Lex; John H Morris
Journal:  PLoS Comput Biol       Date:  2019-09-26       Impact factor: 4.475

  5 in total

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