Molecular Simulation Of Several Important Proteins

From the nineties of the 20th century, advance in computer science, medicine chemistry, molecular biology and computational chemistry have made protein simulation become a well-established and important research area. And protein simulation has become a powerful tool for biology experiments and drug design. In the current thesis, I have carried out homology modeling of cyclin-dependent kinase 10 (CDK10), Cyp2s1, Cyp2f1 and phosphomannose isomerase (PMI). The modeling structures have been optimized by molecular mechanism optimization and molecular dynamics simulation, and then docking studies with substrates and inhibitors based on the modeling structures have been performed. The main results are summarised as follows:: 1. Theoretical study on cyclin-dependent kinase 10. In this study, the three dimensional (3D) structure of CDK10 has been modeled by homology modeling and it was optimized by molecular mechanism optimization and molecular dynamics simulation. The docking studies were performed on the basis of CDK10 3D structure. The results indicate that: a) the residues Asp94, Lys39, Tyr21 and Thr20 are key residues of the binding site in CDK10; b) the residues Lys39 and Asp152 are the key residues in the docking with Flavopiridol. c) The residues Glu89, Cys91, Tyr90 and Val124 are the key residues in the...