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Open Access Software

BioShell-Threading: versatile Monte Carlo package for protein 3D threading

Pawel Gniewek12, Andrzej Kolinski1, Andrzej Kloczkowski23 and Dominik Gront1*

Author Affiliations

1 Laboratory of Theory of Biopolymers, Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland

2 Battelle Center for Mathematical Medicine, The Research Institute at Nationwide Children’s Hospital, 700 Childrens Drive, Columbus, OH 43205, USA

3 Department of Pediatrics, The Ohio State University

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BMC Bioinformatics 2014, 15:22  doi:10.1186/1471-2105-15-22

Published: 20 January 2014

Abstract

Background

The comparative modeling approach to protein structure prediction inherently relies on a template structure. Before building a model such a template protein has to be found and aligned with the query sequence. Any error made on this stage may dramatically affects the quality of result. There is a need, therefore, to develop accurate and sensitive alignment protocols.

Results

BioShell threading software is a versatile tool for aligning protein structures, protein sequences or sequence profiles and query sequences to a template structures. The software is also capable of sub-optimal alignment generation. It can be executed as an application from the UNIX command line, or as a set of Java classes called from a script or a Java application. The implemented Monte Carlo search engine greatly facilitates the development and benchmarking of new alignment scoring schemes even when the functions exhibit non-deterministic polynomial-time complexity.

Conclusions

Numerical experiments indicate that the new threading application offers template detection abilities and provides much better alignments than other methods. The package along with documentation and examples is available at: http://bioshell.pl/threading3d webcite.