Patent US6188965B1 successfully refreshed from Google Patents.
US6188965B1
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Apparatus and method for automated protein design
Assignee: California Institute of Technology
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Filing: 1998-04-10
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Granted: 2001-02-13
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Expires: 2018-04-10
Abstract
Abstract The present invention relates to apparatus and methods for quantitative protein design and optimization.
Inventors
- 👤 Stephen L. Mayo
- 👤 Bassil I. Dahiyat
- 👤 D. Benjamin Gordon
- 👤 Arthur Street
Bibliographic Details
Application Number
—
Jurisdiction
US
Data Source
google_patents
Last Synchronized
2026-11-04 09:39
CPC Classifications
C; C12; C12N; C12N15/00; C12N15/09; C12N15/10; C12N15/1034; C12N15/1089; C07; C07K; C07K1/00; C07K1/003; C07K14/00; C07K14/001; G; G16; G16B; G16B15/00; G16B15/20; G16B20/00; G16B20/50; G16B30/00
Claims Analysis
Total Claims: 18
Claim 1
Independent Claim
125 words
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.
Claim 2
Independent Claim
125 words
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.
Claim 3
Independent Claim
128 words
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.
Claim 4
Independent Claim
128 words
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.
Claim 5
Dependent Claim
14 words
A method according to claim 2 wherein said analyzing step comprises a DEE computation.
Claim 6
Dependent Claim
27 words
A method according to claim 1 or 2 wherein said set of protein sequences optimized for at least one scoring function comprises the globally optimal protein sequence.
Claim 7
Dependent Claim
24 words
A method according to claim 1 or 3 wherein said DEE computation is selected from the group consisting of original DEE and Goldstein DEE.
Claim 8
Dependent Claim
48 words
A method according to claim 1 or 2 wherein said scoring function is selected from the group consisting of a Van der Waals potential scoring function, a hydrogen bond potential scoring function, an atomic salvation scoring function, an electrostatic scoring function and a secondary structure propensity scoring function.
Claim 9
Dependent Claim
21 words
A method according to claim 1 or 2 wherein said analyzing step includes the use of at least two scoring functions.
Claim 10
Dependent Claim
21 words
A method according to claim 1 or 2 wherein said analyzing step includes the use of at least three scoring functions.
Claim 11
Dependent Claim
21 words
A method according to claim 1 or 2 wherein said analyzing step includes the use of at least four scoring functions.
Claim 12
Dependent Claim
19 words
A method according to claim 1 or 2 further comprising experimentally testing at least one member of said set.
Claim 13
Dependent Claim
37 words
A method according to claim 4 further comprising the step of: generating a rank ordered list of additional sequences from said globally optimal protein sequence, wherein said additional sequences are optimized for at least one scoring function.
Claim 14
Dependent Claim
17 words
A method according to claim 11 wherein said generating includes the use of a Monte Carlo search.
Claim 15
Dependent Claim
15 words
A method according to claim 2 wherein said analyzing step comprises a Monte Carlo computation.
Claim 16
Dependent Claim
29 words
A method according to claim 11 further comprising the step of: testing some or all of said protein sequences from said ordered list to produce potential energy test results.
Claim 17
Dependent Claim
25 words
A method according to claim 14 further comprising the step of: analyzing the correspondence between said potential energy test results and theoretical potential energy data.
Claim 18
Dependent Claim
26 words
A method according to claim 11 , wherein said experimentally testing comprises testing for stability or function of said at least one member of said set.
References Cited (Backward Citations)
No citation records indexed.
USPTO Annuity & Maintenance Windows
| Annuity Stage | Window Opens | Payment Deadline | Surcharge Period Until | Estimated Fee | Status |
|---|---|---|---|---|---|
| 3.5 Years (Year 4) | 2004-02-13 | 2004-08-14 | 2005-02-13 | $2000.00 | Window Closed / Lapsed |
| 7.5 Years (Year 8) | 2008-02-13 | 2008-08-14 | 2009-02-13 | $3760.00 | Window Closed / Lapsed |
| 11.5 Years (Year 12) | 2012-02-13 | 2012-08-14 | 2013-02-13 | $7700.00 | Window Closed / Lapsed |