LoopIng: a template-based tool for predicting the structure of protein loops.

Handle URI:
http://hdl.handle.net/10754/596798
Title:
LoopIng: a template-based tool for predicting the structure of protein loops.
Authors:
Messih, Mario Abdel; Lepore, Rosalba; Tramontano, Anna
Abstract:
Predicting the structure of protein loops is very challenging, mainly because they are not necessarily subject to strong evolutionary pressure. This implies that, unlike the rest of the protein, standard homology modeling techniques are not very effective in modeling their structure. However, loops are often involved in protein function, hence inferring their structure is important for predicting protein structure as well as function.We describe a method, LoopIng, based on the Random Forest automated learning technique, which, given a target loop, selects a structural template for it from a database of loop candidates. Compared to the most recently available methods, LoopIng is able to achieve similar accuracy for short loops (4-10 residues) and significant enhancements for long loops (11-20 residues). The quality of the predictions is robust to errors that unavoidably affect the stem regions when these are modeled. The method returns a confidence score for the predicted template loops and has the advantage of being very fast (on average: 1 min/loop).www.biocomputing.it/loopinganna.tramontano@uniroma1.itSupplementary data are available at Bioinformatics online.
Citation:
Messih MA, Lepore R, Tramontano A (2015) LoopIng: a template-based tool for predicting the structure of protein loops. Bioinformatics: btv438. Available: http://dx.doi.org/10.1093/bioinformatics/btv438.
Publisher:
Oxford University Press (OUP)
Journal:
Bioinformatics
KAUST Grant Number:
KUK-I1-012-43
Issue Date:
6-Aug-2015
DOI:
10.1093/bioinformatics/btv438
PubMed ID:
26249814
PubMed Central ID:
PMC4653384
Type:
Article
ISSN:
1367-4803; 1460-2059
Sponsors:
KAUST Award No. KUK-I1-012-43 made by King Abdullah University of Science and Technology (KAUST) and PRIN No. 20108XYHJS.
Appears in Collections:
Publications Acknowledging KAUST Support

Full metadata record

DC FieldValue Language
dc.contributor.authorMessih, Mario Abdelen
dc.contributor.authorLepore, Rosalbaen
dc.contributor.authorTramontano, Annaen
dc.date.accessioned2016-02-21T08:50:54Zen
dc.date.available2016-02-21T08:50:54Zen
dc.date.issued2015-08-06en
dc.identifier.citationMessih MA, Lepore R, Tramontano A (2015) LoopIng: a template-based tool for predicting the structure of protein loops. Bioinformatics: btv438. Available: http://dx.doi.org/10.1093/bioinformatics/btv438.en
dc.identifier.issn1367-4803en
dc.identifier.issn1460-2059en
dc.identifier.pmid26249814en
dc.identifier.doi10.1093/bioinformatics/btv438en
dc.identifier.urihttp://hdl.handle.net/10754/596798en
dc.description.abstractPredicting the structure of protein loops is very challenging, mainly because they are not necessarily subject to strong evolutionary pressure. This implies that, unlike the rest of the protein, standard homology modeling techniques are not very effective in modeling their structure. However, loops are often involved in protein function, hence inferring their structure is important for predicting protein structure as well as function.We describe a method, LoopIng, based on the Random Forest automated learning technique, which, given a target loop, selects a structural template for it from a database of loop candidates. Compared to the most recently available methods, LoopIng is able to achieve similar accuracy for short loops (4-10 residues) and significant enhancements for long loops (11-20 residues). The quality of the predictions is robust to errors that unavoidably affect the stem regions when these are modeled. The method returns a confidence score for the predicted template loops and has the advantage of being very fast (on average: 1 min/loop).www.biocomputing.it/loopinganna.tramontano@uniroma1.itSupplementary data are available at Bioinformatics online.en
dc.description.sponsorshipKAUST Award No. KUK-I1-012-43 made by King Abdullah University of Science and Technology (KAUST) and PRIN No. 20108XYHJS.en
dc.publisherOxford University Press (OUP)en
dc.rightsThis is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.comen
dc.rights.urihttp://creativecommons.org/licenses/by-nc/4.0/en
dc.titleLoopIng: a template-based tool for predicting the structure of protein loops.en
dc.typeArticleen
dc.identifier.journalBioinformaticsen
dc.identifier.pmcidPMC4653384en
dc.contributor.institutionDepartment of Physics, Sapienza University, 00185 Rome, Italy and.en
dc.contributor.institutionDepartment of Physics, Sapienza University, 00185 Rome, Italy and Istituto Pasteur-Fondazione Cenci Bolognetti, Viale Regina Elena 291, 00161 Rome, Italy.en
kaust.grant.numberKUK-I1-012-43en

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