Protein structure prediction with parallel algorithms orthogonal to parallel platforms

• Grant number: 17/25410-8
• Support Opportunities: Scholarships in Brazil - Scientific Initiation
• Start date: March 01, 2018
• End date: February 28, 2019
• Field of knowledge: Physical Sciences and Mathematics - Computer Science - Computing Methodologies and Techniques
• Principal Investigator: Paulo Sérgio Lopes de Souza
• Grantee: Matheus Henrique Junqueira Saldanha
• Host Institution: Instituto de Ciências Matemáticas e de Computação (ICMC). Universidade de São Paulo (USP). São Carlos , SP, Brazil
• Associated research grant: 13/07375-0 - CeMEAI - Center for Mathematical Sciences Applied to Industry, AP.CEPID

Abstract

Due to the abundance and importance of proteins, a greater knowledge about these molecules is known to be of great interest to science. However, laboratory experiments for studying them are expensive and lengthy, which led to the arising of studies on computational methods for predicting the behavior of proteins, which includes its tridimensional structure (3D). The problem of determining the 3D structure of a protein based on its amino acid sequence is NP-complete, and attempts to solve this problem with sequential algorithms are shown to be insufficient, which indicates a clear need for applying parallel computing in such problem. In this project, parallel algorithms for prediction of protein structures, found in the literature, will be investigated in an effort to find opportunities for adapting them to different parallel platforms. Thereafter, a set of algorithms will be elaborated such that it is diverse in terms of the parallel architectures and parallel programming models used. The set will be implemented, evaluated and made publicly available, so as to support the development of more elaborate prediction algorithms that use a collection of algorithms as a means to achieve better predictions. (AU)

Scientific publications

(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)

JUNQUEIRA SALDANHA, MATHEUS HENRIQUE; LOPES DE SOUZA, PAULO SERGIO; RODRIGUES, JMF; CARDOSO, PJS; MONTEIRO, J; LAM, R; KRZHIZHANOVSKAYA, VV; LEES, MH; DONGARRA, JJ; SLOOT, PMA. High Performance Algorithms for Counting Collisions and Pairwise Interactions. COMPUTATIONAL SCIENCE - ICCS 2019, PT I, v. 11536, p. 15-pg., 2019-01-01. (17/25410-8, 13/07375-0)