Methods and systems for molecular modeling
OwnerPhil G. Campbell, Alexander P. Cohen +5inventors
InventorsPhil G. Campbell, Alexander P. Cohen, Lauren A. Ernst, John Ernsthausen, Daniel L. Farkas, William Galbraith, Meir Israelowitz
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Abstract
The present invention is in part directed molecular modeling. In one aspect, a method for determining a structure of a protein is provided, comprising determining the minimum excluded volume of said protein. In another aspect, a method for identifying molecules is provided. In yet another aspect, a computer product is provided for determining the structure of a protein.
Claims23
A method for determining the tertiary structure of a protein comprising:
- providing a protein having a known primary structure;
- and
- determining the minimum excluded volume of said protein.
A method for determining a structure of a protein comprising determining a minimum excluded volume of at least two amino acids in said protein.
A method for identifying molecules which interact with a target protein comprising:
- (a) determining the minimum excluded volume of each amino acid in said target protein;
- (b) determining the lowest free energy of said protein complexed to a small molecule selected from a library of small molecules;
- (c) repeating (b) to identify the small molecule that provides the lowest free energy of said complex;
- and
- selecting the small molecule that provides the lowest free energy.
A method for rational drug design comprising:
- providing a protein having a known ligand binding site;
- and
- determining a minimum excluded volume of said ligand binding site;
- determining a lowest potential energy of said ligand binding site complexed to a small molecule selected from a library of small molecules;
- identifying the small molecule that provides the lowest free energy of said complex;
- and
- selecting the small molecule that provides the lowest free energy.
A method for determining a structure of a protein comprising:
- i) representing one or more polypeptide sequences using a series of constant arclengths;
- ii) selecting an angle which minimizes the volume around one arclength;
- iii) selecting an angle which minimizes the volume around an arclength associated with the arc length in ii);
- iv) iterating ii) and iii) along a polypeptide chain.
A computer product for determining the structure of a protein, the product disposed on a computer readable medium, and including instructions a causing a processor to:
- minimize the volume of amino acids in a polypeptide chain.
A system comprising a processor and instructions for causing a processor to minimize the volume of amino acids in a polypeptide chain.
Dependencies are inferred from the claim text.