PROPOSAL
PROPOSAL (PROtein comparison through Probabilistic Optimal Structure local ALignment) is a Gibbs sampling algorithm for multiple local alignment of 3D protein structures. PROPOSAL can produce biologically significant alignments in reasonable running time, even for large input instances.
Download
Before downloading, be sure to have Java installed. The sources are available upon request.
Application
JAR file to run PROPOSAL from command line (all platforms)
JAR file for the Java 2D application of PROPOSAL. It includes the 3D visualization of structures and alignments with JMol (all platforms).
Test Datasets
Documentation
To run PROPOSAL from command line please refer to the file README.txt contained in PROPOSAL_comm.zip
References
If you use GASOLINE for reasearch purpose, please cite the following paper:
- Micale G, Pulvirenti A, Giugno R, Ferro A (2014). Proteins comparison through probabilistic optimal structure local alignment. Frontiers in Genetics 5(302), doi: 10.3389/fgene.2014.00302 (link)
About
Authors
Dept. of Clinical and Experimental Medicine
University of Catania
gmicale@dmi.unict.it Alfredo Pulvirenti
Dept. of Clinical and Experimental Medicine
University of Catania
apulvirenti@dmi.unict.it
Dept. of Computer Science
University of Verona
rosalba.giugno@univr.it Alfredo Ferro
Dept. of Clinical and Experimental Medicine
University of Catania
ferro@dmi.unict.it
Contacts
If you have any trouble with the software, you want to report any bug or you need the source code, please contact: gmicale@dmi.unict.it and apulvirenti@dmi.unict.it
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