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DC Field | Value | Language |
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dc.contributor.author | Mendonca, Matheus R. de | - |
dc.contributor.author | Rizzi, Leandro G. | - |
dc.contributor.author | Contessoto, Vinicius | - |
dc.contributor.author | Leite, Vitor Barbanti Pereira | - |
dc.contributor.author | Alves, Nelson A. | - |
dc.date.accessioned | 2014-12-03T13:11:08Z | - |
dc.date.accessioned | 2016-10-25T20:12:16Z | - |
dc.date.available | 2014-12-03T13:11:08Z | - |
dc.date.available | 2016-10-25T20:12:16Z | - |
dc.date.issued | 2014-01-01 | - |
dc.identifier | http://dx.doi.org/10.1002/prot.24381 | - |
dc.identifier.citation | Proteins-structure Function And Bioinformatics. Hoboken: Wiley-blackwell, v. 82, n. 1, p. 119-129, 2014. | - |
dc.identifier.issn | 0887-3585 | - |
dc.identifier.uri | http://hdl.handle.net/11449/112900 | - |
dc.identifier.uri | http://acervodigital.unesp.br/handle/11449/112900 | - |
dc.description.abstract | A number of studies have demonstrated that simple elastic network models can reproduce experimental B-factors, providing insights into the structure-function properties of proteins. Here, we report a study on how to improve an elastic network model and explore its performance by predicting the experimental B-factors. Elastic network models are built on the experimental C coordinates, and they only take the pairs of C atoms within a given cutoff distance r(c) into account. These models describe the interactions by elastic springs with the same force constant. We have developed a method based on numerical simulations with a simple coarse-grained force field, to attribute weights to these spring constants. This method considers the time that two C atoms remain connected in the network during partial unfolding, establishing a means of measuring the strength of each link. We examined two different coarse-grained force fields and explored the computation of these weights by unfolding the native structures. Proteins 2014; 82:119-129. (c) 2013 Wiley Periodicals, Inc. | en |
dc.description.sponsorship | LCCA-Laboratory of Advanced Scientific Computation of the University of Sao Paulo | - |
dc.description.sponsorship | Center for Scientific Computing (NCC/GridUNESP) of the Sao Paulo State University (UNESP) | - |
dc.format.extent | 119-129 | - |
dc.language.iso | eng | - |
dc.publisher | Wiley-Blackwell | - |
dc.source | Web of Science | - |
dc.subject | normal mode analysis | en |
dc.subject | GNM | en |
dc.subject | pfGNM | en |
dc.subject | WCN | en |
dc.subject | B-factor | en |
dc.subject | vibrational dynamics | en |
dc.title | Inferring a weighted elastic network from partial unfolding with coarse-grained simulations | en |
dc.type | outro | - |
dc.contributor.institution | Universidade de São Paulo (USP) | - |
dc.contributor.institution | Universidade Estadual Paulista (UNESP) | - |
dc.description.affiliation | Univ Sao Paulo, FFCLRP, Dept Fis, BR-14040901 Ribeirao Preto, SP, Brazil | - |
dc.description.affiliation | Univ Estadual Paulista, IBILCE, Dept Fis, BR-15054000 Sao Jose Do Rio Preto, SP, Brazil | - |
dc.description.affiliationUnesp | Univ Estadual Paulista, IBILCE, Dept Fis, BR-15054000 Sao Jose Do Rio Preto, SP, Brazil | - |
dc.identifier.doi | 10.1002/prot.24381 | - |
dc.identifier.wos | WOS:000328090900011 | - |
dc.rights.accessRights | Acesso aberto | - |
dc.relation.ispartof | Proteins: Structure, Function and Bioinformatics | - |
Appears in Collections: | Artigos, TCCs, Teses e Dissertações da Unesp |
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