[Chimera-users] Evolutional-based analysis in Chimera

James Starlight jmsstarlight at gmail.com
Wed May 25 06:12:24 PDT 2016

Dear Chimera Users!

For my particular analysis I have 2 homologue membrane proteins (one
is bacterial, and another one- mammalian cytocrome-C oxydase) each
bound to same smaller (ligand) protein called for simplicity
"the_guy". For that particular case the conservation in sequence of
both protein is quite low however 1) the overall fold of both proteins
especially within the membrane-embedded region as well as 2)
ligand-bound (which is mostly the water exposed loops) region are
quite similar.
Now using some Chimera  tool I need to estimate binding interfaces of
two homologous proteins  in terms of the conservation of the resides
involved in binding of the_guy. Then I need to make more complex task-
performing the same evolutional analysis but comparing 2 ensembles
extracted from the MD trajectory represent simulation of binding of
each of the protein with the_guy to track correlations of the
statistics between the residues involved in the binding during MD as
well as overall conservation for particular fold. Does the
"Evolutionary tracing" might be useful here?

Thanks for help!


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