Current Synthetic and Systems Biology
Open Access

Abstract

Non-Linear and Misleading Template Scoring Criteria: Root Cause of Protein Modelling Inaccuracies

Ashish Runthala

Template based protein modelling is currently the most accurate as well as trustworthy method for predicting the correct protein conformations to bridge the constantly increasing gap between the number of experimentally solved protein structures and the count of protein sequences. Our best knowledge based prediction algorithms employing the templates are not highly proficient of consistently selecting the best scoring template(s) to construct a highly accurate protein model. Mutually contrary nature of generic and currently employed template assessment and selection scores further makes this essential modelling step a very tricky and fluky business. Precisely, the article briefly investigates and justifies the impact of fundamentally allowed degree of freedom of a template selection measure on the accuracy of constructed protein models. Several logical guidelines, normally overlooked in a protein modelling task, are analyzed and should be routinely considered. A more reliable and robust scoring measure is thus mandatorily required to select the best possible available template for constructing the most accurate target conformation.