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What and Who

A Molecular Dynamic Approach Based on Knowledge-based Force Function for Prediction of Protein Structure

Ali Ghaffaari
University of Tehran
PhD Application Talk
AG 1, AG 2, AG 3, AG 4, AG 5, SWS, RG1, MMCI  
Public Audience

Date, Time and Location

Monday, 19 May 2014
75 Minutes
E1 4


Understanding of how a polypeptide is able to fold to its native structure is one of the central problems in molecular biology. Molecular dynamics simulations have become a powerful technique to study protein folding problem. In this technique, physical energy functions are widely used. The main disadvantage of these functions is that they require substantial computational resources. On the other hand, current force fields are not accurate enough to be able to fold a protein on a computer. In this study, we formulated a force field which is obtained from statistical contact preferences within the known protein structures. An estimate of the inter-atomic forces between any two atoms can be calculated using this force field. We are developing an MD tool in order to simulate the evolution of the proteins using this pairwise potential. Since the structure of folded proteins reflects the energy of the interaction of all their components as well as solvent effects, we expect better result of finding native state in comparison with the other force fields based on the fundamental analysis of the forces between the particles referred to as physical energy function. In our method, after a preprocessing phase, inter-atomic forces can be derived from a table-like data structure during simulation. Therefore this method also has an advantage that it can be run in a reasonable time.


Jennifer Gerling
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Jennifer Gerling, 05/15/2014 11:35
Jennifer Gerling, 05/15/2014 11:30 -- Created document.