Developing a methodology to simulate flexible complete docking and specific mutation in the primary structure and its applications to study interaction protein-protein, protein-ligand and resistance of pathogenesis and drugs

• Grant number: 10/09306-7
• Support Opportunities: Regular Research Grants
• Start date: September 01, 2010
• End date: August 31, 2012
• Field of knowledge: Biological Sciences - Biophysics - Molecular Biophysics
• Principal Investigator: Ana Lígia Barbour Scott
• Grantee: Ana Lígia Barbour Scott
• Host Institution: Centro de Matemática, Computação e Cognição (CMCC). Universidade Federal do ABC (UFABC). Ministério da Educação (Brasil). Santo André , SP, Brazil
• Associated researchers: Antonio Sergio Kimus Braz

Abstract

There are several methods/software to simulate molecular docking; those that have been implemented use different force fields and algorithms. Different approximations exist depending which type of degrees of freedom are to be considered, and this includes rigid docking where protein and ligand are rigid, semi-flexible where only a selected set of side-chains of the protein are allowed to move, or fully flexible where all the protein (including the backbone) and the ligand are allowed to change their conformation The mains objectives of this research project are: extend and improve the methodology GANM developed by a regular research project (Proc. 2007/05696-2). The new version (extended) will be able to simulate docking of protein-protein and it will be able study the effect of specific mutations in the context of docking. (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)

LIBERATO, MICHELLE S.; KOGIKOSKI, JR., SERGIO; SILVA, EMERSON R.; COUTINHO-NETO, MAURICIO D.; SCOTT, LUIS P. B.; SILVA, RICARDO H.; OLIVEIRA, JR., VANI X.; ANDO, ROMULO A.; ALVES, WENDEL A.. Self-Assembly of Arg-Phe Nanostructures via the Solid-Vapor Phase Method. Journal of Physical Chemistry B, v. 117, n. 3, p. 733-740, JAN 24 2013. (12/01933-8, 10/09306-7, 05/60596-8, 09/12153-0, 08/57805-2)