Predicting protein ligand binding motions with the conformation explorer.

ABSTRACT:

Background

Knowledge of the structure of proteins bound to known or potential ligands is crucial for biological understanding and drug design. Often the 3D structure of the protein is available in some conformation, but binding the ligand of interest may involve a large scale conformational change which is difficult to predict with existing methods.

Results

We describe how to generate ligand binding conformations of proteins that move by hinge bending, the largest class of motions. First, we predict the location of the hinge between domains. Second, we apply an Euler rotation to one of the domains about the hinge point. Third, we compute a short-time dynamical trajectory using Molecular Dynamics to equilibrate the protein and ligand and correct unnatural atomic positions. Fo

SUBMITTER: Flores SC 

PROVIDER: S-EPMC3354956 | biostudies-literature | 2011 Oct

REPOSITORIES: biostudies-literature