Accurate prediction of protein dihedral angles through conditional random field

Abstract

Identifying local conformational changes induced by subtle differences on amino acid sequences is critical in exploring the functional variations of the proteins. In this study, we designed a computational scheme to predict the dihedral angle variations for different amino acid sequences by using conditional random field. This computational tool achieved an accuracy of 87% and 84% in 10-fold cross validation in a large data set for ϕ and ψ, respectively. The prediction accuracies of ϕ and ψ are positively correlated to each other for most of the 20 types of amino acids. Helical amino acids can achieve higher prediction accuracy in general, while amino acids in beet sheet have higher accuracy at specific angular regions. The prediction accuracy of ϕ is negatively correlated with amino acid flexibility represented by Vihinen Index. The prediction accuracy of ϕ can also be negatively correlated with angle distribution dispersion.

Keywords

conditional random field / flexibility / angle distribution dispersion

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2014 Higher Education Press and Springer-Verlag Berlin Heidelberg