Computational Methods Applied to Bio-molecular Structure Determination from the Perspective of Distance Geometry

• Grant number: 24/21786-7
• Support Opportunities: Scholarships in Brazil - Post-Doctoral
• Start date: April 01, 2025
• End date: March 31, 2027
• Field of knowledge: Physical Sciences and Mathematics - Mathematics - Applied Mathematics
• Principal Investigator: Carlile Campos Lavor
• Grantee: Wagner Alan Aparecido da Rocha
• Host Institution: Instituto de Matemática, Estatística e Computação Científica (IMECC). Universidade Estadual de Campinas (UNICAMP). Campinas , SP, Brazil
• Associated research grant: 23/08706-1 - Numerical optimization, AP.TEM

Abstract

The field of structural biology has made significant progress in determining protein structures, which is crucial for understanding their biological functions and molecular activities, with important implications for health and biotechnology. Over the past decades, this area has produced numerous protein structures, primarily using continuous optimization approaches and local techniques. This project aims to develop and implement algorithms based on discrete optimization methods grounded in the theory of Distance Geometry, which has already demonstrated superior performance compared to continuous approaches when applied to toy problems. The mathematical problem addressed is known as the Molecular Distance Geometry Problem (MDGP), which investigates the feasibility of embedding a graph, constructed from interatomic distances obtained through Nuclear Magnetic Resonance (NMR), into three-dimensional space. The project's first phase involves mathematical modeling in collaboration with structural biology researchers, followed by theoretical formalization and computational implementation. The results will be evaluated based on widely recognized metrics for protein structure comparison.