Comparative evaluation of commercially available homology modelling tools: A structural bioinformatics perspective

Abstract

Background

Structure based drug design has revolutionised the way new drug molecules are being looked for. A very important technique in this process is homology modelling of protein structures. Although a number of protocols are proposed by a number of research groups, yet a comparative assessment is desired to identify the relative merits and demerits of these programs. Comparative assessment of various homology modelling tools was evaluated using prediction of structure of B-domain of factor V.

Methods

The methods employed, here, for comparative assessment were ESyPred3D, SWISS MODEL, PHYRE2 and YASARA. The criteria for selection of these tools were their popularity among users and level of automation. All these are completely automated and require only protein sequence or alignments as input. These tools were fast and the results were obtained within few hours.

Results

To evaluate the various models of the protein structures, we carried out exhaustive evaluation through “WHATif” and “QMEAN”. The parameters included the bond angle, bond length, coarse packing quality control, collision symmetry, omega angle, hand check dihedrals etc.

Conclusion

According to our study YASARA emerged as best performer.