HOMA: HOmology Modeling Automatically
HOMA We have described an automatic approach for homology modeling using restrained molecular dynamics and simulated annealing procedures Li et al, Protein Science, 6, 956-970, 1997
This method uses distances calculated from the template structure to determine the structure of a homologous protein. This software calculates distances between atoms in the template structure from a pdb file and then, uses a sequence alignment file to select the distance constraints involving homologous atoms.
HOMA is a user-friendly, web-based implementation of this algorithm. HOMA requires an alignment of the template sequence against the query sequence and a template coordinate file to carry out the calculations. The results include a bundle of models as well as analysis of the model quality.
HOMA is available at http://www-nmr.cabm.rutgers.edu/HOMA/ or http://hyper.quifis.uv.es/HOMA/index.html, under password protection.