Osmar Norberto De Souza
Posters & Accepted Abstracts: J Comput Sci Syst Biol
Although the protein folding/structure problem is known since the early 1950s, the protein folding/structure prediction (PSP) problem was presented about 52 years ago and continues unsolved. PSP constitutes a major challenge in the structural biology and bioinformatics research fields. As a contribution to possible solutions to this problem, we have developed the CReF (Central Residue Fragment-Based) method for the prediction of the approximate 3-D structure of proteins. CReF can predict correctly the elements of secondary structure of proteins but not their native fold. For that reason, we employ molecular dynamics (MD) simulations with restraints on the main-chain torsion angle of regular secondary structures, and at different temperatures, to refine the CReF predictions. In this presentation, we will report improvements in our refinement protocols. Refinements with an RMSD of as low as 1.3 ├?┬? for a 53 amino acid residues protein can be attained in the 50 ns time scale, a far smaller molecular dynamics time scale than most current folding prediction protocols. Also, we will show results for small, medium and large proteins belonging to the ├?┬▒, ├?┬▓, and ├?┬▒/├?┬▓ structural classes.
Journal of Computer Science & Systems Biology received 2279 citations as per Google Scholar report