Distance geometry and protein loop modeling.

Labiak, Rodrigo; Lavor, Carlile; Souza, Michael

Labiak, Rodrigo; Lavor, Carlile; Souza, Michael.

Afiliação

Labiak R; Department of Mathematics, University of Campinas, Campinas, Brazil.
Lavor C; Department of Applied Mathematics, University of Campinas, Campinas, Brazil.
Souza M; Department of Applied Mathematics, Federal University of Ceara, Fortaleza, Brazil.

J Comput Chem ; 43(5): 349-358, 2022 02 15.

Article em En | MEDLINE | ID: mdl-34904248

RESUMO

Due to the role of loops in protein function, loop modeling is an important problem in computational biology. We present a new approach to loop modeling based on a combinatorial version of distance geometry, where the search space of the associated problem is represented by a binary tree and a branch-and-prune method is defined to explore it, following an atomic ordering previously given. This ordering is used to calculate the coordinates of atoms from the positions of its predecessors. In addition to the theoretical development, computational results are presented to illustrate the advantage of the proposed method, compared with another approach of the literature. Our algorithm is freely available at https://github.com/michaelsouza/bpl.

Assuntos

Proteínas/química; Algoritmos; Biologia Computacional; Modelos Moleculares; Conformação Proteica

Palavras-chave

branch-and-prune; distance geometry; protein loop modeling

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Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Proteínas Idioma: En Revista: J Comput Chem Assunto da revista: QUIMICA Ano de publicação: 2022 Tipo de documento: Article País de afiliação: Brasil País de publicação: Estados Unidos

Texto completo

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