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.
Before downloading, be sure to have Java installed. The sources are available upon request.
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).
If you use GASOLINE for reasearch purpose, please cite the following paper: