Name:STFCAPP
Description:Simulation of three-dimensional folding by prediction of critical amino acid positions in proteins
Abstract:This application lies in the field of Bioinformatics and more precisely, in the domain of ab initio prediction of protein folding.<BR/>From the point of view of Biology and Biophysics, it simulates the initial stages of the folding process of a polypeptide chain into a unique, globular, stable and biologically functional protein. By using only amino acid sequence data, it provides a set of amino acid residues, called MIRs, which play a critical role in the folding process. The knowledge of these residues from the amino acid sequence is important for a successful prediction of protein structure.<BR/>The practical importance of ab initio prediction methods is justified by the continuously increasing number of newly discovered proteins. The structures of all these proteins cannot be rapidly solved experimentally from Crystallography or NMR.<BR/>From a mathematical point of view, the application is a discrete-space Monte-Carlo numerical simulation. The program input consists of the amino acid (a.a.) sequence of the protein and an interaction matrix, which assigns an energy value to each pair of a.a., according to their type and distance in three-dimensional space. Starting from a random initial conformation, the total energy of the chain is computed. At each Monte-Carlo step, an a.a. is randomly chosen to move to a new position. The resulting new chain conformation is accepted or rejected by comparing the new and old total energies, following a standard Metropolis criterion. Every 100 Monte-Carlo (MC) steps, for each residue, the number of its spatial neighbours is calculated. At the end of the simulation, the time mean value of this number is extracted. The above described process is repeated 100 times for 100 different initial conformations and a global mean value is calculated for each residue. This number is rounded to the nearest integer and is called NCN, for Non-Covalent Neighbours. NCN varies from 1 to 9. When NCN ≥ 6 for an a.a., this latter is called a MIR, for Mostly Interacting Residues. The MIRs constitute the
Created:2010-05-01
Last updated:2010-05-01
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