Dear Pat
Yes, AMPLE does it's own, purely structure-based, alignment of the
homologs provided using GESAMT. You provide a directory of structures to
work with and, crucially, give AMPLE the
-homologs True
flag so that it knows the inputs have different sequences (unlike in
modelling mode), and need to be dealt with accordingly.
There's more explanation and example files here
http://ample.readthedocs.io/en/latest/examples/rst/homologs.html#example-dist-homologs
In this mode AMPLE first finds the common core shared by all inputs and
then produces graded further truncations of that with different side
chain treatments. This sampling is often necessary in the hardest cases.
What this means, however, is if the input set are ultra-diverse, then
the GESAMT shared common core can be quite small. It can therefore also
be worth trying a smaller set of not quite so diverse structures which
share a somewhat larger core structure.
Best wishes
Daniel
On 20/07/17 23:13, Patrick Loll wrote:
I’m intrigued by the prospect of using AMPLE to test multiple distant homologs
in a MR problem. I’ve used HHPRED to identify about 20 high-probability
homologs of known structure, each of which has about 20-25% identity with the
unknown protein. However, it’s not clear to me from the documentation whether
the program will use the alignments from HHPRED, and, if so, how I should
provide that information.
Or does AMPLE perform its own alignment? I.e., do I simply point the program to
a directory containing 20 different PDB files and stand back?
Thanks for any insights.
Cheers,
Pat
---------------------------------------------------------------------------------------
Patrick J. Loll, Ph. D.
Professor of Biochemistry & Molecular Biology
Drexel University College of Medicine
Room 10-102 New College Building
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Dr Daniel John Rigden Tel:(+44) 151 795 4467
Institute of Integrative Biology FAX:(+44) 151 795 4406
Room 101, Biosciences Building
University of Liverpool http://pcwww.liverpool.ac.uk/~drigden/
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