Journal of Proteomics & Bioinformatics
Open Access
ISSN: 0974-276X
ISSN: 0974-276X
Kawano Takayuki and Takeshi Kikuchi
Ritsumeikan University, Japan
Posters & Accepted Abstracts: J Proteomics Bioinform
In a drug discovery process, the binding free energy between a protein and a ligand is often estimated by a computational technique. These methods still require further improvement, in spite of the innovation of new techniques. The purpose of this study is to establish a new in silico method with low cost and no parameter tuning. Here, we calculate relative binding free energies on the basis of the free energy variational principle (FEVP), with minimization and molecular dynamics simulation protocols. We apply this technique to the cyclin dependent kinase 2 (CDK2) ligand inhibitor systems of which IC50 values were reported. In the construction of the initial complex structure, we use several CDK2 structures with various ligands. From the results, it was found that FEVP method can predict to some extent with high accuracy.