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US 6,188,965 B1Granted
Apparatus and method for automated protein design
AssigneeCalifornia Institute of Technology
InventorsStephen L. Mayo, Bassil I. Dahiyat, D. Benjamin Gordon, Arthur Street
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Abstract
The present invention relates to apparatus and methods for quantitative protein design and optimization.
Claims16
A method executed by a computer under the control of a program, said computer including a memory for storing said program, said method comprising the steps of:
- (A) receiving a protein backbone structure with variable residue positions;
- (B) establishing a group of potential rotamers for each of said variable residue positions, wherein the group of potential rotamers for at least one of said variable residue position has a rotamer selected from each of at least two different amino acid side chains;
- and
- (C) analyzing the interaction of each of said rotamers with all or part of the remainder of said protein to generate a set of protein sequences optimized for at least one scoring function,
- wherein said analyzing step includes a Dead-End Elimination (DEE) computation.
2 more elements
A method executed by a computer the control of a program, said computer including a memory for storing said program said method comprising the steps of:
- (A) receiving a protein backbone structure with variable residue positions;
- (B) classifying each variable residue position as either a core, surface or boundary residue;
- (C) establishing a group of potential rotamers for each of said variable residue positions, wherein the group of potential rotamers for at least one of sad variable residue positions has A rotamer selected from each of at least two different amino acid side chains;
- and
- (D) analyzing the interaction of each of said rotamers with all or part of the remainder of said protein to generate a set of protein sequences optimized for at least one scoring function.
2 more elements
Dependencies are inferred from the claim text.