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dc.contributor.authorIacoangeli, Alfredo
dc.contributor.authorMarcatili, Paolo
dc.contributor.authorTramontano, Anna
dc.date.accessioned2021-11-03T07:25:46Z
dc.date.available2021-11-03T07:25:46Z
dc.date.issued2015
dc.identifier.citationIacoangeli, A., Marcatili, P., & Tramontano, A. (2015). Exploiting Homology Information in Nontemplate Based Prediction of Protein Structures. Journal of Chemical Theory and Computation, 11(10), 5045–5051. doi:10.1021/acs.jctc.5b00371
dc.identifier.issn1549-9626
dc.identifier.issn1549-9618
dc.identifier.doi10.1021/acs.jctc.5b00371
dc.identifier.urihttp://hdl.handle.net/10754/673082
dc.description.abstractIn this paper we describe a novel strategy for exploring the conformational space of proteins and show that this leads to better models for proteins the structure of which is not amenable to template based methods. Our strategy is based on the assumption that the energy global minimum of homologous proteins must correspond to similar conformations, while the precise profiles of their energy landscape, and consequently the positions of the local minima, are likely to be different. In line with this hypothesis, we apply a replica exchange Monte Carlo simulation protocol that, rather than using different parameters for each parallel simulation, uses the sequences of homologous proteins. We show that our results are competitive with respect to alternative methods, including those producing the best model for each of the analyzed targets in the CASP10 (10th Critical Assessment of techniques for protein Structure Prediction) experiment free modeling category.
dc.description.sponsorshipThis work was supported by the King Abdullah University of Science and Technology (KAUST), Award Number KUK-I1-012-43 and PRIN 20108XYHJS.
dc.publisherAMER CHEMICAL SOC
dc.relation.urlhttps://pubs.acs.org/doi/10.1021/acs.jctc.5b00371
dc.titleExploiting Homology Information in Nontemplate Based Prediction of Protein Structures
dc.typeArticle
dc.identifier.journalJOURNAL OF CHEMICAL THEORY AND COMPUTATION
dc.identifier.wosutWOS:000362921700051
dc.contributor.institutionUniv Roma La Sapienza, Dept Phys, I-00185 Rome, Italy
dc.contributor.institutionUniv Roma La Sapienza, Ist Pasteur Fdn Cenci Bolognetti, I-00185 Rome, Italy
dc.identifier.volume11
dc.identifier.issue10
dc.identifier.pages5045-5051
kaust.grant.numberKUK-I1-012-43
kaust.grant.numberPRIN 20108XYHJS
dc.identifier.eid2-s2.0-84944207005


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