Analysis of the effects of simulation parameters in molecular docking

• Grant number: 22/00562-8
• Support Opportunities: Scholarships in Brazil - Scientific Initiation
• Start date: February 01, 2022
• End date: December 31, 2022
• Field of knowledge: Engineering - Chemical Engineering
• Principal Investigator: Pedro de Alcântara Pessôa Filho
• Grantee: Pedro Henrique Callil Soares
• Host Institution: Escola Politécnica (EP). Universidade de São Paulo (USP). São Paulo , SP, Brazil
• Associated research grant: 14/21252-0 - Equilibrium and production processes of biofuels and bioproducts, AP.TEM

Abstract

Molecular docking is a simulation technique that aims to predict the conformation and affinity of the bond between the receptor, a macromolecule, and the ligand, usually a small molecule, finding applications in the food and pharmaceutical industries, among others. Compared to other molecular simulation techniques, such as molecular dynamics, docking simulations are considerably faster, due to the use of several simplifications. However, the results obtained are less precise, since the simulation is less faithful to physical principles. Therefore, some care must be taken when choosing which simplification shall be adopted (as the flexibility of receptor or ligand) and when defining the preprocessing of the molecules (with addition or subtraction of hydrogen atoms, the inclusion of charges, or the protonation of the active sites of the receptor, for example). Besides, the choice of algorithm might lead to different results, and, therefore, must be carefully defined. The project aims to analyze those differences, through the analysis of the differences among the results of molecular docking simulations with distinct parameters, applied to a predefined set of identical pairs receptor-ligand, with real conformation and affinity known.(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)

CALLIL-SOARES, PEDRO HENRIQUE; BIASI, LILIAN CAROLINE KRAMER; PESSOA FILHO, PEDRO DE ALCANTARA. Effect of preprocessing and simulation parameters on the performance of molecular docking studies. Journal of Molecular Modeling, v. 29, n. 8, p. 15-pg., 2023-08-01. (22/00562-8, 14/21252-0, 21/09028-1)