Evidence map›Paper›PMID 19656955›Full record

ArticleNucleic acids research2009

VENN, a tool for titrating sequence conservation onto protein structures.

Jay Vyas, Michael R Gryk, Martin R Schiller

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nucleic acids research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.

0numbers the graph read from it
0cells of the map it votes in
8citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

8 citing papers in PubMed.

  1. Article
  2. CCProf: exploring conformational change profile of proteins.Database : the journal of biological databases and curation · 2016
    Article
  3. Article
  4. Article
  5. An Open-Source Sandbox for Increasing the Accessibility of Functional Programming to the Bioinformatics and Scientific Communities.Proceedings of the ... International Conference on Information Technology: New Generations. International Conference on Information Technology: New Generations · 2012
    Article
  6. Iterative Development of an Application to Support Nuclear Magnetic Resonance Data Analysis of Proteins.Proceedings of the ... International Conference on Information Technology: New Generations. International Conference on Information Technology: New Generations · 2011
    Article
  7. SciReader enables reading of medical content with instantaneous definitions.BMC medical informatics and decision making · 2011
    Article
  8. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

3 authors.

Jay VyasDepartment of Molecular, Microbial and Structural Biology, University of Connecticut Health Center, Farmington, CT 06030-3305, USA.
Michael R Gryk
Martin R Schiller

Funding

Building motif lexiconsR01GM079689 · NIGMS · UNIVERSITY OF NEVADA LAS VEGAS · PI SCHILLER, MARTIN R · 2007 to 2010
$1.1M
Identification of short functional motifs as potential drug targets for HIVR21AI078708 · NIAID · UNIVERSITY OF NEVADA LAS VEGAS · PI SCHILLER, MARTIN R · 2008 to 2009
$368k
Database-driven software for biological NMR analysisR21EB001496 · NIBIB · UNIVERSITY OF CONNECTICUT SCH OF MED/DNT · PI GRYK, MICHAEL R · 2005 to 2006
$327k
NIAID NIH HHS AI078708NIBIB NIH HHS EB001496NIGMS NIH HHS GM079689
6 · The paper itself

Abstract

Residue conservation is an important, established method for inferring protein function, modularity and specificity. It is important to recognize that it is the 3D spatial orientation of residues that drives sequence conservation. Considering this, we have built a new computational tool, VENN that allows researchers to interactively and graphically titrate sequence homology onto surface representations of protein structures. Our proposed titration strategies reveal critical details that are not readily identified using other existing tools. Analyses of a bZIP transcription factor and receptor recognition of Fibroblast Growth Factor using VENN revealed key specificity determinants. Weblink: http://sbtools.uchc.edu/venn/.

Indexed as

Protein ConformationSequence Homology, Amino AcidSoftwareAmino Acid SequenceCCAAT-Enhancer-Binding Protein-betaConserved SequenceFibroblast Growth Factor 8HumansModels, MolecularCCAAT-Enhancer-Binding Protein-betaFibroblast Growth Factor 8

Identifiers

PMID19656955
PMCPMC2764419

What OpenQuestion holds

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LicenceCC BY-NC
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.