Literature DB >> 24336804

DIVE: a data intensive visualization engine.

Dennis Bromley1, Steven J Rysavy, Robert Su, Rudesh D Toofanny, Tom Schmidlin, Valerie Daggett.   

Abstract

SUMMARY: Modern scientific investigation is generating increasingly larger datasets, yet analyzing these data with current tools is challenging. DIVE is a software framework intended to facilitate big data analysis and reduce the time to scientific insight. Here, we present features of the framework and demonstrate DIVE's application to the Dynameomics project, looking specifically at two proteins.
AVAILABILITY AND IMPLEMENTATION: Binaries and documentation are available at http://www.dynameomics.org/DIVE/DIVESetup.exe.

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Year:  2013        PMID： 24336804      PMCID： PMC3928528          DOI： 10.1093/bioinformatics/btt721

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


  11 in total

1.  Cytoscape: a software environment for integrated models of biomolecular interaction networks.

Authors:  Paul Shannon; Andrew Markiel; Owen Ozier; Nitin S Baliga; Jonathan T Wang; Daniel Ramage; Nada Amin; Benno Schwikowski; Trey Ideker
Journal:  Genome Res       Date:  2003-11       Impact factor: 9.043

Review 2.  Structure, folding, and misfolding of Cu,Zn superoxide dismutase in amyotrophic lateral sclerosis.

Authors:  Rishi Rakhit; Avijit Chakrabartty
Journal:  Biochim Biophys Acta       Date:  2006-05-22

3.  The Protein Data Bank: a computer-based archival file for macromolecular structures.

Authors:  F C Bernstein; T F Koetzle; G J Williams; E F Meyer; M D Brice; J R Rodgers; O Kennard; T Shimanouchi; M Tasumi
Journal:  J Mol Biol       Date:  1977-05-25       Impact factor: 5.469

4.  Dynameomics: a comprehensive database of protein dynamics.

Authors:  Marc W van der Kamp; R Dustin Schaeffer; Amanda L Jonsson; Alexander D Scouras; Andrew M Simms; Rudesh D Toofanny; Noah C Benson; Peter C Anderson; Eric D Merkley; Steven Rysavy; Dennis Bromley; David A C Beck; Valerie Daggett
Journal:  Structure       Date:  2010-03-14       Impact factor: 5.006

5.  DIVE: a graph-based visual-analytics framework for big data.

Authors:  Steven J Rysavy; Dennis Bromley; Valerie Daggett
Journal:  IEEE Comput Graph Appl       Date:  2014 Mar-Apr       Impact factor: 2.088

6.  Structural consequences of mutations to the α-tocopherol transfer protein associated with the neurodegenerative disease ataxia with vitamin E deficiency.

Authors:  Dennis Bromley; Peter C Anderson; Valerie Daggett
Journal:  Biochemistry       Date:  2013-06-10       Impact factor: 3.162

7.  Protein Simulation Data in the Relational Model.

Authors:  Andrew M Simms; Valerie Daggett
Journal:  J Supercomput       Date:  2011-09-29       Impact factor: 2.474

8.  Structural changes to monomeric CuZn superoxide dismutase caused by the familial amyotrophic lateral sclerosis-associated mutation A4V.

Authors:  Tom Schmidlin; Brian K Kennedy; Valerie Daggett
Journal:  Biophys J       Date:  2009-09-16       Impact factor: 4.033

9.  Targeted rescue of a destabilized mutant of p53 by an in silico screened drug.

Authors:  Frank M Boeckler; Andreas C Joerger; Gaurav Jaggi; Trevor J Rutherford; Dmitry B Veprintsev; Alan R Fersht
Journal:  Proc Natl Acad Sci U S A       Date:  2008-07-23       Impact factor: 11.205

10.  Structural basis for understanding oncogenic p53 mutations and designing rescue drugs.

Authors:  Andreas C Joerger; Hwee Ching Ang; Alan R Fersht
Journal:  Proc Natl Acad Sci U S A       Date:  2006-10-02       Impact factor: 11.205
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  3 in total

Review 1.  Big data in medicine is driving big changes.

Authors:  F Martin-Sanchez; K Verspoor
Journal:  Yearb Med Inform       Date:  2014-08-15

2.  DIVE: a graph-based visual-analytics framework for big data.

Authors:  Steven J Rysavy; Dennis Bromley; Valerie Daggett
Journal:  IEEE Comput Graph Appl       Date:  2014 Mar-Apr       Impact factor: 2.088

3.  An in silico algorithm for identifying stabilizing pockets in proteins: test case, the Y220C mutant of the p53 tumor suppressor protein.

Authors:  Dennis Bromley; Matthias R Bauer; Alan R Fersht; Valerie Daggett
Journal:  Protein Eng Des Sel       Date:  2016-08-08       Impact factor: 1.650
  3 in total

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