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.
Claims40
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 structure of a desired target protein, said protein structure comprising:
- i) a protein template structure comprising a protein backbone structure and at least one non-variable residue;
- and
- ii) a plurality of variable residue positions;
- (B) establishing a group of potential amino acid side chains for a plurality of said variable residue positions of said protein;
- and
- (C) analyzing the interaction of all or part of each of said potential amino acid side chains from said group with all or part of the remainder of said protein structure to generate a set of optimized proteins sequences, wherein said analyzing step includes a Dead-End Elimination (DEE) computation.
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 structure of a desired target protein, said protein structure comprising:
- i) a protein template structure comprising a protein backbone structure and at least one non-variable residue;
- and
- ii) a plurality of variable residue positions;
- (B) classifying each variable residue position as either a core, surface or boundary residue;
- (C) establishing a group of potential amino acid side chains for a plurality of said variable residue positions of said protein;
- and
- (D) analyzing the interaction of all or part of each of said potential amino acid side chains from said group with all or part of the remainder of said protein structure to generate a set of optimized proteins 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 structure of a desired target protein, said protein structure comprising:
- i) a protein template structure comprising a protein backbone structure and at least one non-variable residue;
- and
- ii) a plurality of variable residue positions;
- (B) establishing a group of potential amino acid side chains for each of said variable residue positions, wherein the group of potential amino acids side chains for at least one of said variable residue position has an amino acid side chains selected from each of at least two different amino acid side chains;
- and
- (C) analyzing the interaction of all or part of each of said potential amino acid side chains from said group with all or part of the remainder of said protein structure to generate a set of optimized proteins 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 structure of a desired target protein, said protein structure comprising:
- i) a protein template structure comprising a protein backbone structure and at least one non-variable residue;
- and
- ii) a plurality of variable residue positions;
- (B) establishing a group of potential amino acid side chains for a plurality of variable residue positions of said protein, wherein at least one of said amino acid side chains is from a hydrophilic amino acid;
- and
- (C) analyzing the interaction of all or part of each of said potential amino acid side chains from said group with all or part of said protein structure to generate a set of optimized proteins sequences, wherein said analyzing step includes the use of at least one scoring function.
A method according to 1, 10, 11, or 12 wherein step (c) comprises a second group for a second variable position which has a second set of at least two amino acid side chains.
A method according to 1, 10, 11, or 12 wherein said non-variable residues are fixed.
A method according to 1, 10, 11, or 12 wherein said non-variable residues are floated.
Dependencies are inferred from the claim text.