Predicting of protein surface accessibility with information theory

ABSTRACT A new, simple method based on information theory is introduced to predict the solvent accessibility of amino acid residues in vari-ous states defined by their different thresholds. Prediction is achieved by the application of informa-tion obtained from a single amino acid position or pair-information for a window of seventeen amino acids around the desired residue. Results obtained by pairwise information values are better than re-sults from single amino acids. This reinforces the effect of the local environment on the accessibility of amino acid residues. The prediction accuracy of this method in a jackknife test system for two and three states is better than 70 and 60%, respectively. A comparison of the results with those reported by others involving the same data set also testifies to a better prediction accuracy in our case. Proteins 2001;42:452–459. © 2001 Wiley-Liss, Inc. Key words: protein structure prediction; solvent ac-cessibility; hydropathy scale; local envi-ronment; pairwise informatio