Quick Reliable Exploration of the PDB Universe Seeks a New Template Search Algorithm
Sunil Nahata and Ashish Runthala*
Department of Biological Sciences, Birla Institute of Technology & Science, Pilani, Rajasthan, India
- *Corresponding Author:
- Ashish Runthala
Department of Biological Sciences
Birla Institute of Technology & Science, Pilani, Rajasthan, India
Tel: +911596 515-817
E-mail: [email protected]
Received date: October 10, 2016; Accepted date: October 27, 2016; Published date: October 31, 2016
Citation: Nahata S, Runthala A (2016) Quick Reliable Exploration of the PDB Universe Seeks a New Template Search Algorithm. J Data Mining Genomics Proteomics 7:206. doi: 10.4172/2153-0602.1000206
Copyright: © 2016 Nahata S, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Near-native protein structure prediction through Template Based Modelling (TBM) has been a major realistic goal of structural biology for several years. The TBM algorithms require the best-set of templates for a target protein sequence to maximally cover it and construct its correct topology. However, the accuracy of such prediction algorithms suffers from the algorithmic and logical problems of our template search measures which fail to quickly screen reliable structures for a target sequence. In this study, we employ the culled PDB95 dataset of 41,967 templates to predict the CASP10 target T0752 models for assessing the efficiency of the usually employ search engines PSI-BLAST and HHPred. Our analysis presents a detailed study in order to open new vistas for improving the accuracy of TBM prediction methodologies. It reveals weaknesses of most popular template search measures and thereby briefly provides a significant insight into the qualities of a foreseen template search algorithm to illustrate the need for a more reliable template search algorithm.