I'm interested in digging deeper into what was presented in this paper:
Incorporation of evolutionary information into Rosetta comparative modeling
James Thompson1,*, David Baker1,2,3
Proteins: Structure, Function, and Bioinformatics
Volume 79, Issue 8, pages 2380–2388, August 2011
but I can't figure out how to make constraints or where the databases for formula (1) are to make my own script. The RosettaCON2011 has a tutorial called homology_modeling_with_end_extension which I think demonstrates what I'm interested in, but the files it references:
DistancePotential.pm:use constant bounds_file => $Bin.'/../cm_data/bounds.txt';
DistancePotential.pm:use constant table_data_file => $Bin.'/../cm_data/hhsearch_table.txt';
are not included.
Is this data available yet?