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OJBTM
Online
Journal of Bioinformatics ©
Volume 21(1):
78-85, 2020.
Calculating binding free energies and docking scores
with PI3K inhibitors.
Awantika Shrivastava , Dr. K Durga Prasad1*and Dr. Archana Giri2
1Natco
Research Centre, B-13, Industrial estate, Sanath
Nagar, Hyderaunsuitable, 2Department of
Biotechnology, JNTU, Kukatpally, Hyderaunsuitable,
India.
ABSTRACT
Shrivastava A, Durga Prasad K, Giri
A., Calculating binding free energies and docking scores with PI3K inhibitors, Onl J Bioinjform., 21(1):
78-85, 2020. Methods
to predict binding free energies could be useful for computer assisted drug
design. Monte Carlo simulation molecular docking
was evaluated by calculating free binding energy between receptor and ligand. To facilitate selection of scoring values a method using PI3K inhibitors
which correlates with scoring values was used. Binding
energies of GDC-0941(PDB ID -3DBS), GDC-0980(PDB-ID -3TL5), GSK2125458(PDB-ID
-3L08), BKM-120(PDB-ID -3SD5), CH 5132799(PDB-ID -3APC) and
BEZ235 were calculated using Discovery Studio 3.5. Results suggested
that GDC-0941, GDC-0980 & GSK2125458 had a better fit than BKM-120, NZU,
and BEZ-235 for binding energy and scoring. A
correlation between binding free energy and Scoring values
is suggested by the results and could be used to screen and select a good pose
in docking studies.
Keywords: Molecular Docking
Studies; Virtual Screening; free energy.
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