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Bioinformatics Advance Access originally published online on January 16, 2009
Bioinformatics 2009 25(5):676-677; doi:10.1093/bioinformatics/btp034
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© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

CPSP-web-tools: a server for 3D lattice protein studies

Martin Mann 1,*, Cameron Smith 1, Mohamad Rabbath 1, Marlien Edwards 2, Sebastian Will 1 and Rolf Backofen 1,*

1Bioinformatics Group, University of Freiburg, Georges-Köhler-Allee 106, 79016 Freiburg, Germany and 2German University in Cairo, Department of Computer Science, 5th Settlement New Cairo City, Cairo, Egypt

*To whom correspondence should be addressed.


  Abstract

Summary: Studies on proteins are often restricted to highly simplified models to face the immense computational complexity of the associated problems. Constraint-based protein structure prediction (CPSP) tools is a package of very fast algorithms for ab initio optimal structure prediction and related problems in 3D HP-models [cubic and face centered cubic (FCC)]. Here, we present CPSP-web-tools, an interactive online interface of these programs for their immediate use. They include the first method for the direct prediction of optimal energies and structures in 3D HP side-chain models. This newest extension of the CPSP approach is described here for the first time.

Availability and Implementation: Free access at http://cpsp.informatik.uni-freiburg.de

Contact: cpsp{at}informatik.uni-freiburg.de; cpsp{at}informatik.uni-freiburg.de

Associate Editor: Dmitrij Frishman

Received on December 23, 2008; revised on January 9, 2009; accepted on January 10, 2009

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