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US 6,708,120 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.
Claims8
A computer readable memory to direct a computer to function in a specified manner, comprising:
- a) a side chain module to receive a group of potential rotamers for residue positions of a protein backbone structure for a target protein;
- and
- b) an analyzing module to analyze 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 module includes a ranking module, said ranking module comprising a Dead-End Elimination (DEE) computation.
A computer readable memory to direct a computer to function in a specified manner, comprising:
- a) a side chain module to receive a group of potential rotamers for variable residue positions of a protein backbone structure for a target protein, wherein at least one variable position has a set of rotamers from at least two different amino acid side chains;
- b) a scoring module to analyze 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;
- and
- c) a ranking module comprising a Dead-End Elimination (DEE) computation.
1 more element
A computer readable memory to direct a computer to function in a specified manner, comprising:
- a) a side chain module to receive a group of potential amino acids for variable residue positions of a protein backbone structure for a target protein, wherein at least one variable position has a set of amino acids from at least two different amino acid side chains;
- b) a scoring module to analyze the interaction of each of said amino acids with all or part of the remainder of said protein to generate a set of optimized protein sequences;
- and
- c) a ranking module comprising a Dead-End Elimination (DEE) computation.
1 more element
Dependencies are inferred from the claim text.