TITLE:
Evaluation of CDK6 and p16/INK4a-Derived Peptides Interaction
AUTHORS:
Andrey Kazennov, Andrey Alekseenko, Vladimir Bozhenko, Tatiana Kulinich, Nikolay Shuvalov, Yaroslav Kholodov
KEYWORDS:
Cyclin-Dependent Kinases; Molecular Dynamics; Umbrella Sampling; GPU; SASA
JOURNAL NAME:
Computational Molecular Bioscience,
Vol.3 No.3,
August
22,
2013
ABSTRACT: The goal of this work is the development of novel peptides with high efficacy of inhibiting activity of CDK6/CyclinD complex. The peptides were derived from primary sequence of P16 protein and its homologues. The interactions between CDK6 and P16/INK4a-derived peptides are studied with molecular dynamics simulation employing umbrella sampling method. The SASA implicit solvent model was used for simulation, which was accelerated using NVIDIA GPUs.