Drift coefficient and simulation of amino acid-solvent interactions for proteins whose main chain have \alpha-helical secondary structures

The formation of multiple helical-linear segments of a polymer in a solvent is investigated analytically. Winding probability functions for diffusive polypeptides is obtained for a drift coefficient f(s) involving Fourier cosine function of the variable s along the chain. Applications to protein chains are explored where the formation of α-helices between linear segments is compared to the conformation of myoglobin (4mbn) found in the Protein Data Bank (PDB). The results generated are also comparable to the results of the well-known APSSP2 secondary structure prediction server of Raghava which employed a sophisticated Example Based Learning (EBL) approach with a combination of neural network and nearest neighbour algorithm. Considering the large amount of data from Protein Data Bank (PDB), we can conveniently predict or mimic the structure of 28 Wilson I. Barredo and Henry P. Aringa other α-helical proteins in solvents with much less computing times which can be used to explore the protein folding problem.