Fast procedure for reconstruction of full-atom protein models from reduced representations

TitleFast procedure for reconstruction of full-atom protein models from reduced representations
Publication TypeJournal Article
Year of Publication2008
AuthorsRotkiewicz P, Skolnick J
JournalJ Comput Chem
Volume29
Issue9
Pagination1460-5
Date Published2008 Jul 15
ISSN1096-987X
KeywordsAlgorithms, Computer Simulation, Crystallography, Models, Biological, Predictive Value of Tests, Protein Conformation, Proteins, Thermodynamics
Abstract

We introduce PULCHRA, a fast and robust method for the reconstruction of full-atom protein models starting from a reduced protein representation. The algorithm is particularly suitable as an intermediate step between coarse-grained model-based structure prediction and applications requiring an all-atom structure, such as molecular dynamics, protein-ligand docking, structure-based function prediction, or assessment of quality of the predicted structure. The accuracy of the method was tested on a set of high-resolution crystallographic structures as well as on a set of low-resolution protein decoys generated by a protein structure prediction algorithm TASSER. The method is implemented as a standalone program that is available for download from http://cssb.biology.gatech.edu/skolnick/files/PULCHRA.

Alternate JournalJournal of Computational Chemistry

© Michal Brylinski
This website is hosted at the CCT