QSLiMFinder: improved short linear motif prediction using specific query protein data

Bioinformatics
Nicolas PalopoliRichard J Edwards

Abstract

The sensitivity of de novo short linear motif (SLiM) prediction is limited by the number of patterns (the motif space) being assessed for enrichment. QSLiMFinder uses specific query protein information to restrict the motif space and thereby increase the sensitivity and specificity of predictions. QSLiMFinder was extensively benchmarked using known SLiM-containing proteins and simulated protein interaction datasets of real human proteins. Exploiting prior knowledge of a query protein likely to be involved in a SLiM-mediated interaction increased the proportion of true positives correctly returned and reduced the proportion of datasets returning a false positive prediction. The biggest improvement was seen if a short region of the query protein flanking the interaction site was known. All the tools and data used in this study, including QSLiMFinder and the SLiMBench benchmarking software, are freely available under a GNU license as part of SLiMSuite, at: http://bioware.soton.ac.uk.

Associated Software

References

Dec 11, 1999·Nucleic Acids Research·H M BermanP E Bourne
Jun 10, 2005·FEBS Letters·Victor Neduva, Robert B Russell
Jul 21, 2006·Nucleic Acids Research·Norman E DaveyRichard J Edwards
Sep 12, 2006·Current Opinion in Biotechnology·Victor Neduva, Robert B Russell
Apr 1, 2008·Bioinformatics·Richard J EdwardsDenis C Shields
May 30, 2008·Frontiers in Bioscience : a Journal and Virtual Library·Francesca DiellaToby J Gibson
Jul 4, 2008·PloS One·Amelie Stein, Patrick Aloy
May 26, 2010·Nucleic Acids Research·Norman E DaveyRichard J Edwards
May 27, 2010·PLoS Computational Biology·Amelie Stein, Patrick Aloy
Jun 3, 2010·Frontiers in Bioscience (Landmark Edition)·Norman E DaveyDenis C Shields
Dec 15, 2010·Trends in Biochemical Sciences·Norman E DaveyToby J Gibson
Apr 26, 2011·Current Opinion in Structural Biology·Peter Tompa
Apr 26, 2011·Current Opinion in Structural Biology·M Madan BabuJörg Gsponer
Sep 1, 2011·Molecular BioSystems·Richard J EdwardsDenis C Shields
Sep 13, 2011·Molecular BioSystems·Norman E DaveyToby J Gibson
Nov 24, 2011·Nucleic Acids Research·Holger DinkelToby J Gibson
Apr 27, 2012·IUBMB Life·Rita Pancsa, Monika Fuxreiter
Oct 2, 2013·Nucleic Acids Research·Roberto MoscaPatrick Aloy
Nov 12, 2013·Nucleic Acids Research·Holger DinkelToby J Gibson
Jan 6, 2015·Methods in Molecular Biology·Richard J Edwards, Nicolas Palopoli

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Methods Mentioned

BETA
two-hybrid

Software Mentioned

QSLiMFinder Query SLiMFinder
SLiMFinder
QSLiMFinder
Nomask
QSLiMFinder SN
SLiMMaker
SLiMSearch
SLiMBench
pro
FIRE

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