BioShell-Threading: versatile Monte Carlo package for protein 3D threading.
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.
Pawel
P
Gniewek
Andrzej
A
Kolinski
Andrzej
A
Kloczkowski
Laboratory of Theory of Biopolymers, Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland. dgront@chem.uw.edu.pl.
Dominik
D
Gront
D000465:Algorithms; D000595:Amino Acid Sequence; D019295:Computational Biology; D003198:Computer Simulation; D008958:Models, Molecular; D009010:Monte Carlo Method; D011506:Proteins / Q000737:chemistry*; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software
D011506:Proteins