Improving the sampling process in the interval Branch-and-Prune algorithm for the discretizable molecular distance geometry problem

Autor(es)

Lavor, Carlile ^[1] ; Souza, Michael ^[2] ; Carvalho, Luiz M. ^[3] ; Goncalves, Douglas S. ^[4] ; Mucherino, Antonio ^[5]

Afiliação do(s) autor(es)

^[1] Univ Estadual Campinas, Dept Appl Math IMECC UNICAMP, BR-13081970 Campinas, SP - Brazil

^[2] Univ Fed Ceara, Dept Stat & Appl Math, BR-60440900 Fortaleza, Ceara - Brazil

^[3] Univ Estado Rio De Janeiro, Dept Appl Math, BR-20559900 Rio De Janeiro, RJ - Brazil

^[4] Univ Fed Santa Catarina, Dept Math, BR-88040900 Florianopolis, SC - Brazil

^[5] Univ Rennes 1, IRISA, F-35042 Rennes - France

• Tipo de documento: Artigo Científico
• Fonte: Applied Mathematics and Computation; v. 389, JAN 15 2021.
• Citações Web of Science: 3

Resumo

Protein structure determination using Nuclear Magnetic Resonance (NMR) experiments is one of the most important applications of Distance Geometry, called the Molecular Distance Geometry Problem (MDGP). Using special atomic orders on the protein molecule, the MDGP can be solved iteratively using a combinatorial method, called Branch-and-Prune (BP). In order to deal with uncertainties of NMR data, there is an extension of the BP algorithm, called interval BP, where the idea is to sample values from the interval distances associated to such uncertainties. We propose a method to improve this sampling process, by reducing the interval of uncertain distances before taking the samples. All the mathematical details necessary to understand the proposal and its implementation are provided, along with some computational experiments that indicate the proposed strategy improves the interval BP algorithm. (C) 2020 Elsevier Inc. All rights reserved. (AU)

• Processo FAPESP: 17/22465-6 - Uma Abordagem em 5D para o Cálculo de Estrutura de Proteínas
• Beneficiário: Carlile Campos Lavor
• Modalidade de apoio: Auxílio à Pesquisa - Regular
• Processo FAPESP: 19/20047-8 - Geometria de distâncias e álgebra de Clifford para o cálculo de estrutura 3D de proteínas
• Beneficiário: Carlile Campos Lavor
• Modalidade de apoio: Bolsas no Exterior - Pesquisa