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:
OWL requires Java 1.6 or newer (available from http://java.sun.com).
The latest development version of OWL can be found in the GIT repository.
How to check out the code using GIT:
git clone https://github.com/eppic-team/owl
For questions about development and usage of OWL please sign up to the Developer's mailing list.
Projects where OWL has been used:
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).
Protein interface classification by evolutionary analysis Jose M Duarte, Adam Srebniak, Martin A Schärer, Guido Capitani. BMC Bioinformatics 2012, 13:334.
See also the EPPIC web server