Apparatus and method for automated protein design
AssigneeCalifornia Institute of Technology
InventorsStephen L. Mayo, Bassil I. Dahiyat, D. Benjamin Gordon, Arthur Street, Yaoying Su
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Abstract
The present invention relates to apparatus and methods for quantitative protein design and optimization.
Claims23
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) altering at least one supersecondary structure parameter value of said protein backbone structure;
- (C) establishing a group of potential rotamers for each of said vahable 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 diferent amino acid side chains;
- and
- (D) analyzing the interaction of each of said rotamers with all or part of the remainder of said protein backbone structure to generate a set of optimized protein sequences wherein said analyzing step includes a Dead-End Elimination (DEE) canmputation.
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) altering at least one supersecondary structure parameter value of said protein backbone structure;
- (C) classifying each variable residue position as either a core, surface or boundary residue;
- (D) establishing a group of potential rotamers for each of said variable residue positions, wherein the group of potential rotaters for at least one of said variable residue position has a rotamer selected from each of at least two dilrerent amino acid side chains;
- and
- (E) analyzing the interaction of each of said rotamers with all or part of the remainder of said protein to generate a set of optimized protein sequences.
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) altering at least one supersecondary structure parameter value of said protein backbone structure;
- (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 said variable residue position has a rotamer selected from each of at least two diferent amino acid side chains;
- and
- (D) analyzing the interaction of each of said rotamers with all or part of the remainder of said protein backbone structure to generate a set of optimized protein sequences, wherein said analyzing step includes:
- i. a Dead-End Elimination (DEE) computation;
- and,
- ii. at least one scoring function selected from the group consisting of a Van der Waals potential scoring function, a hydrogen bond potential scoring fanction, an atomic solvation scoring function, an electrostatic scoring function and a secondary structure propensity scoring function.
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) altering at least one supersecondary structure parameter value of said protein backbone structure;
- (C) classifying each variable residue position as either a core, surface or boundary residue;
- (D) 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
- E) analyzing the interaction of each of said rotamers with all or part of the remainder of said protein to generate a set of optimized protein sequences wherein said analyzing step includes:
- i. a Dead-End Elimination (DEE) computation;
- and,
- ii. at least one scoring function selected from the group consisting of a Van der Waals potential scoring function, a hydrogen bond potential scoring function, an atomic solvation scoring function, an electrostatic scoring function and a secondary structure propensity scoring function.
Dependencies are inferred from the claim text.