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OJBTM
Online Journal of Bioinformatics©
Volume 18(3):100-107,
2017.
Calculating binding free energies and docking
scores with PI3K inhibitors.
Awantika Shrivastava,
K Durga Prasad1*and
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 Bioinform., 18(3):100-107, 2017.
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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