Method for modeling and refining molecular structures
OwnerYong Duan, Wei Zhanginventors
Life of this patent
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Abstract
A method for modeling and refining reduction of the side chain size to obtain a smooth energy landscape due to the increased distances between the side chains. The side chains then gradually grow back during molecular dynamics simulations while adjusting to their surrounding driven by the interaction energies. The method of the invention overcomes barriers resulting from tight packing that limit conformational sampling of physics-based models.
Claims22
A method for modeling a molecule having a refined protein structure, comprising the steps of:
- producing a reduced molecular model of a molecule;
- and
- growing said reduced molecular model to a normal size while adjusting to a local environment using a molecular dynamics simulation process.
A method for modeling a molecule having a refined protein structure, comprising the steps of:
- providing a model of a molecule and a local environment in a computer system;
- adjusting a scaling term of an energy function corresponding to said modecule;
- reducing the model to form a reduced molecular model;
- and
- growing said reduced molecular model to a normal size in said local environment, said energy function controlling growth of said reduced molecular model to produce a refined protein structure for said reduced molecular model.
A method for modeling protein side chain assignment, comprising the steps of:
- reducing a high energy barrier associated with a molecule to produce a model of a smooth energy surface in a computer system;
- and
- modeling growth of a protein structure in said computer system by simulating assignments of protein side chains, said assignments being controlled by said model of said smooth energy surface.
Dependencies are inferred from the claim text.