Optimal Length of Fragments for Use in Protein Structure Prediction

T. Higgs, B. Stantic, and M.T. Hoque (Australia)

Keywords

Bioinformatics, Fragment Libraries, and Protein Structure Prediction.

Abstract

Proteins are three-dimensional structures that carry out many of the vital biological functions in organisms. Be cause structure, not amino acid sequence order, carry out certain functions, it is important to understand how pro teins fold. Computational methods for protein structure prediction mentioned in the literature are computationally demanding. To reduce computational demand fragment li braries were introduced. Fragment libraries work by taking short segments of the polypeptide chain and limiting the amount of conformations that will be considered for a par ticular segment. In this paper an extensive analysis towards ļ¬nding the optimal length of fragments contained within fragment libraries was conducted. An extensive analysis was done on protein structures stored in a ORDBMS to exploit its power. Experiments focused on the structural similarity between fragments of identical primary protein sub-sequence within different proteins, and amount of oc currences of similar or closely similar fragments within dif ferent proteins. Experimental results indicate that short to medium sized fragments have stronger structural correla tions with matching fragments within different proteins.

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