active_site_identity.py

[Stefan]

Hi!

For comparison of binding sites of different homology models, I want
to use the script
active_site_identity.py (vers. 3.0) from the script centre. This
script selects all residues of different structures within a certain
radius around a ligand given in the first structure and writes
identity, homology and ribosome-identity scores between pairs of
structures.

My first question is now, for calculating the homology score, what is
the definition of homology? It seems to be calculated by
mm.mmalign_codes_have_identity
(sim[j][k] += mm.mmalign_codes_have_identity(matrix[i][j], matrix[i]
[k]) in def print_homology_matrix) but I could not find any
documentation for this function.

The second question is regarding the definition of the ribosome-
identity score. What is the scientific bases for this score?

Thanks a lot!

Best,
Stefan

[Mike Beachy]

Hi Stefan -

The mmalign_codes_have_identity function identifies whether there's a
positive score in the BLOSUM62 substitution matrix.

I'm not sure about the basis of the ribosome identity score, but I'll
ask around.

Thanks,
Mike

p.s. You'll find that any code from the schrodinger.infra.mm module
will be lacking documentation; all of these functions are wrappers to
C code. Feel free to ask about things here or at he...@schrodinger.com.

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