OWL is a Java library and a set of command line tools for the analysis of biological macromolecules. It provides functionality for analysing protein sequences and structures using built-in algorithms and interfaces to external tools. Particular emphasis is put on the analysis of proteins as contact graphs.
How to use OWL:
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OWL requires Java 1.6 or newer (available from http://java.sun.com).
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The latest development version of OWL can be found in the trunk of the SVN repository.
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How to check out the code using SVN:
svn co svn://bioinformatics.org/svnroot/owl/trunk .More detailed instructions can be found here.
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For questions about development and usage of OWL please sign up to the Developer's mailing list.
Projects where OWL has been used:
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RECONSTRUCT - Protein contact map reconstruction using the TINKER package
Optimal contact definition for reconstruction of Contact Maps.
Jose M Duarte, Rajagopal Sathyapriya, Henning Stehr, Ioannis Filippis and Michael Lappe. BMC Bioinformatics 2010, 11:283.Defining an Essence of Structure Determining Residue Contacts in Proteins. Rajagopal Sathyapriya, Jose M. Duarte, Henning Stehr, Ioannis Filippis, Michael Lappe. PLoS Computational Biology 5(12): e1000584 (2009).
Optimized Null Model for Protein Structure Networks. Tijana Milenkovic, Ioannis Filippis, Michael Lappe, Natasa Przul. PLoS ONE 4(6): e5967 (2009).