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 Title: |
US5436850:
Method to identify protein sequences that fold into a known three-dimensional structure
[ Derwent Title ]
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| Country: |
US United States of America
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| Inventor: |
Eisenberg, David; Los Angeles, CA
Bowie, James U.; Culver City, CA
Luthy, Roland; Los Angeles, CA
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| Assignee: |
The Regents of the University of California, Oakland, CA
other patents from UNIVERSITY OF CALIFORNIA, THE REGENTS OF (599425) (approx. 4,840)
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| Published / Filed: |
1995-07-25
/ 1994-03-28
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| Application Number: |
US1994000218685
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| IPC Code: |
Advanced:
C07K 1/00;
G01N 33/68;
G06F 17/50;
Core:
more...
IPC-7:
C12Q 1/68;
G06F 19/00;
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| ECLA Code: |
G06F19/00C2; C07K1/00; G01N33/68;
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| U.S. Class: |
Current:
703/011;
436/086;
436/089;
Original:
364/496;
364/497;
436/089;
436/086;
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| Field of Search: |
364/498,497,496
435/004,5,69.1,69.7,69.8
436/015,43,86,89
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| Priority Number: |
| 1994-03-28 |
US1994000218685 |
| 1991-07-11 |
US1991000728640 |
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| Abstract: |
A computer-assisted method for identifying protein sequences that fold into a known three-dimensional structure. The inventive method attacks the inverse protein folding problem by finding target sequences that are most compatible with profiles representing the structural environments of the residues in known three-dimensional protein structures. The method starts with a known three-dimensional protein structure and determines three key features of each residue's environment within the structure: (1) the total area of the residue's side-chain that is buried by other protein atoms, inaccessible to solvent; (2) the fraction of the side-chain area that is covered by polar atoms (O, N) or water, and (3) the local secondary structure. Based on these parameters, each residue position is categorized into an environment class. In this manner, a three-dimensional protein structure is converted into a one-dimensional environment string, which represents the environment class of each residue in the folded protein structure. A 3D structure profile table is then created containing score values that represent the frequency of finding any of the 20 common amino acids structures at each position of the environment string. These frequencies are determined from a database of known protein structures and aligned sequences. The method determines the most favorable alignment of a target protein sequence to the residue positions defined by the environment string, and determines a "best fit" alignment score, Sij, for the target sequence. Each target sequence may then be further characterized by a ZScore, which is the number of standard deviations that Sij for the target sequence is above the mean alignment score for other target sequences of similar length.
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| Attorney, Agent or Firm: |
Spensley Horn Jubas & Lubitz ;
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| Primary / Asst. Examiners: |
Trans, Vincent N.;
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| Maintenance Status: |
CC Certificate of Correction issued
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| INPADOC Legal Status: |
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Family Legal Status Report
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| Parent Case: |
This is a continuation of application Ser. No. 07/728,640 filed on Jul. 11, 1991, now abandoned.
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| Designated Country: |
AU CA EP JP
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| Family: |
Show 4 known family members
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First Claim:
Show all 26 claims |
We claim:
1. A computer-assisted method for characterizing the three-dimensional structure of a protein, using a programmed computer comprising a processor, a data storage system, at least one input device, and at least one output device, comprising the steps of:
- (a) generating input data for the programmed computer, including the steps of:
- (1) determining, from the three-dimensional structure of the protein, values for n structural properties P1, P2, . . . Pn for each amino acid residue position of the protein;
- (2) assigning each residue of the protein to one of a plurality of environment classes, based upon the values for the n structural properties P1, P2, . . . Pn for the residue, thereby generating a one-dimensional environment string comprising the environment class of each residue in the three-dimensional protein structure;
- (b) inputting the generated input data into the programmed computer through one of the input devices:
- (c) comparing, by means of the processor, the environment string to a computer database of other proteins of known three-dimensional structure stored in the computer data storage system;
- (d) selecting, using computer methods, analogous three-dimensional protein structures in the computer database;
- (e) outputting to at least one output device the selected analogous three-dimensional protein structures.
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| Background / Summary: |
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| Drawing Descriptions: |
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| Description: |
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| Forward References: |
Show 32 U.S. patent(s) that reference this one
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