title: D2N: Distance to the native.
abstract: Root-mean-square-deviation (RMSD), of computationally-derived protein structures from experimentally determined structures, is a critical index to assessing protein-structure-prediction-algorithms (PSPAs). The development of PSPAs to obtain 0Å RMSD from native structures is considered central to computational biology. However, till date it has been quite challenging to measure how far a predicted protein structure is from its native - in the absence of a known experimental/native structure. In this work, we report the development of a metric "D2N" (distance to the native) - that predicts the "RMSD" of any structure without actually knowing the native structure. By combining physico-chemical properties and known universalities in spatial organization of soluble proteins to develop D2N, we demonstrate the ability to predict the distance of a proposed structure to within ±1.5Ǻ error with a remarkable average accuracy of 93.6% for structures below 5Ǻ from the native. We believe that this work opens up a completely new avenue towards assigning reliable structures to whole proteomes even in the absence of experimentally determined native structures. The D2N tool is freely available at http://www.scfbio-iitd.res.in/software/d2n.jsp.
authors: Kusuma School of Biological Sciences, Indian Institute of Technology, Hauz Khas, New Delhi 110016, India.
authors: Avinash
authors: A
authors: Mishra
authors: Supercomputing Facility for Bioinformatics & Computational Biology, Indian Institute of Technology, Hauz Khas, New Delhi 110016, India.
authors: Prashant Singh
authors: PS
authors: Rana
authors: Kusuma School of Biological Sciences, Indian Institute of Technology, Hauz Khas, New Delhi 110016, India.
authors: Aditya
authors: A
authors: Mittal
authors: Kusuma School of Biological Sciences, Indian Institute of Technology, Hauz Khas, New Delhi 110016, India; Supercomputing Facility for Bioinformatics & Computational Biology, Indian Institute of Technology, Hauz Khas, New Delhi 110016, India; Department of Chemistry, Indian Institute of Technology, Hauz Khas, New Delhi 110016, India. Electronic address: bjayaram@chemistry.iitd.res.in.
authors: B
authors: B
authors: Jayaram
keywords: Decoy; Native; Protein folding; Quality assessment