Distance geometry and protein loop modeling.

Autor: 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.
Jazyk: angličtina
Zdroj: Journal of computational chemistry [J Comput Chem] 2022 Feb 15; Vol. 43 (5), pp. 349-358. Date of Electronic Publication: 2021 Dec 14.
DOI: 10.1002/jcc.26796
Abstrakt: 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.
(© 2021 Wiley Periodicals LLC.)
Databáze: MEDLINE
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