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bioRxiv · 10.1101/192120

Prediction of residue-residue contacts in CASP12 targets from its predicted tertiary structures

Agrawal, P.·Singh, S.·Nagpal, G.·Sethi, D.·Raghava, G. P. S.
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Abstract

One of the challenges in the field of structural proteomics is to predict residue-residue contacts in a protein. It is an integral part of CASP competitions due to its importance in the field of structural biology. This manuscript describes RRCPred 2.0 a method participated in CASP12 and predicted residue-residue contact in targets with high precision. In this approach, firstly 150 predicted protein structures were obtained from CASP12 Stage 2 tarball and ranked using clustering-based quality assessment software. Secondly, residue-residue contacts were assigned in top 10 protein structures based on distance between residues. Finally, residue-residue contacts were predicted in target protein based on consensus/average in top 10 predicted structures. This simple approach performs better than most of CASP12 methods in the categories of TBM and TBM/FM. It ranked 1st in following categories; i) TBM domain on list size L/5, ii) TBM/FM domain on list size L/5 and iii) TBM/FM domain on Top 10. These observations indicate that predicted tertiary structure of a protein can be used for predicting residue-residue contacts in protein with high accuracy.

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Agrawal, P., Singh, S., Nagpal, G., Sethi, D., Raghava, G. P. S.. 2017-09-21. Prediction of residue-residue contacts in CASP12 targets from its predicted tertiary structures. https://doi.org/10.1101/192120

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