Dear Amber
users,
I’m doing
some tests with a short MD and MMPBSA.py for free-energy calculation. In this
test I get the results of free energy of two complexes (a ligand for two
different proteins, respectively).
Analyzing
these results I would like to see if the free energy could help to explain the
specificity of the ligand towards one of the proteins.
The results
are:
Protein1-ligand:
DELTA G
binding: -33.03 + / - 4.11 (std. dev.) 0.08 (Std. err. of mean)
Protein2-ligand:
DELTA G
binding: -26.69 + / - 3.74 (std. dev.) 0.09 (Std err. of mean)
These
results may suggest that the ligand has higher affinity for protein 1. However,
the std. dev values are large so they do not support this assertion. Aren’t
they? Does the interpretation of the results seem consistent with the results
observed?
=======================================
Aldo Segura-Cabrera
Laboratorio de Bioinformática
Centro de Biotecnología Genómica
Instituto Politécnico Nacional
Blvd. Del Maestro esquina Elías Piña, 88710
Reynosa, Tamaulipas, México.
(899)9243627 ext. 87747
e-mail:
asegurac.ipn.mx;
aldosegura.gmail.com
=========================================
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Received on Thu Apr 07 2011 - 13:30:03 PDT
