Computational generation inhibitor-bound conformers of p38 MAP kinase and comparison with experiments.

ABSTRACT: The p38 MAP kinases play a critical role in regulating stress-activated pathways, and serve as molecular targets for controlling inflammatory diseases. Computer-aided efforts for developing p38 inhibitors have been hampered by the necessity to include the enzyme conformational flexibility in ligand docking simulations. A useful strategy in such complicated cases is to perform ensemble-docking provided that a representative set of conformers is available for the target protein either from computations or experiments. We explore here the abilities of two computational approaches, molecular dynamics (MD) simulations and anisotropic network model (ANM) normal mode analysis, for generating potential ligand-bound conformers starting from the apo state of p38, and benchmark them against the space

SUBMITTER: Bakan A 

PROVIDER: S-EPMC4782186 | biostudies-literature | 2011

REPOSITORIES: biostudies-literature