| Full text | |
| Author(s): |
Lavor, Carlile
[1]
;
Souza, Michael
[2]
;
Carvalho, Luiz M.
[3]
;
Goncalves, Douglas S.
[4]
;
Mucherino, Antonio
[5]
Total Authors: 5
|
| Affiliation: | [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
Total Affiliations: 5
|
| Document type: | Journal article |
| Source: | Applied Mathematics and Computation; v. 389, JAN 15 2021. |
| Web of Science Citations: | 3 |
| Abstract | |
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) | |
| FAPESP's process: | 17/22465-6 - A 5D Approach to the Calculation of Protein Structure |
| Grantee: | Carlile Campos Lavor |
| Support Opportunities: | Regular Research Grants |
| FAPESP's process: | 19/20047-8 - Distance geometry and Clifford algebra for 3D protein structure calculation |
| Grantee: | Carlile Campos Lavor |
| Support Opportunities: | Scholarships abroad - Research |