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Online Journal of Bioinformatics ©
Volume 15 (1): 106-113, 2014
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, Hyderabad, 2Department of Biotechnology, JNTU, Kukatpally, Hyderabad, India.
Shrivastava A, Durga Prasad K, Giri A., Calculating binding free energies and docking scores with PI3K inhibitors, Onl J Bioinform., 15(1):106-113, 2014. 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 for docking studies.
Keywords: Molecular Docking Studies; Virtual Screening; free energy.