WO2001092990A3 - Structure-based methods for assessing amino acid variances - Google Patents
Structure-based methods for assessing amino acid variances Download PDFInfo
- Publication number
- WO2001092990A3 WO2001092990A3 PCT/US2001/017351 US0117351W WO0192990A3 WO 2001092990 A3 WO2001092990 A3 WO 2001092990A3 US 0117351 W US0117351 W US 0117351W WO 0192990 A3 WO0192990 A3 WO 0192990A3
- Authority
- WO
- WIPO (PCT)
- Prior art keywords
- amino acid
- protein
- methods
- based methods
- interest
- Prior art date
Links
- 150000001413 amino acids Chemical class 0.000 title abstract 3
- 102000004169 proteins and genes Human genes 0.000 abstract 4
- 108090000623 proteins and genes Proteins 0.000 abstract 4
- 125000000539 amino acid group Chemical group 0.000 abstract 2
- 230000004071 biological effect Effects 0.000 abstract 1
- 230000000694 effects Effects 0.000 abstract 1
Classifications
-
- G—PHYSICS
- G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
- G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
- G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
-
- G—PHYSICS
- G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
- G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
- G16B15/00—ICT specially adapted for analysing two-dimensional or three-dimensional molecular structures, e.g. structural or functional relations or structure alignment
- G16B15/20—Protein or domain folding
-
- G—PHYSICS
- G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
- G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
- G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
- G16B20/20—Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
-
- G—PHYSICS
- G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
- G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
- G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
- G16B30/20—Sequence assembly
-
- G—PHYSICS
- G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
- G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
- G16B15/00—ICT specially adapted for analysing two-dimensional or three-dimensional molecular structures, e.g. structural or functional relations or structure alignment
-
- G—PHYSICS
- G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
- G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
- G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
Landscapes
- Life Sciences & Earth Sciences (AREA)
- Physics & Mathematics (AREA)
- Health & Medical Sciences (AREA)
- Bioinformatics & Cheminformatics (AREA)
- Engineering & Computer Science (AREA)
- Spectroscopy & Molecular Physics (AREA)
- Theoretical Computer Science (AREA)
- Medical Informatics (AREA)
- Biophysics (AREA)
- Bioinformatics & Computational Biology (AREA)
- Biotechnology (AREA)
- Evolutionary Biology (AREA)
- General Health & Medical Sciences (AREA)
- Chemical & Material Sciences (AREA)
- Analytical Chemistry (AREA)
- Proteomics, Peptides & Aminoacids (AREA)
- Genetics & Genomics (AREA)
- Molecular Biology (AREA)
- Crystallography & Structural Chemistry (AREA)
- Investigating Or Analysing Biological Materials (AREA)
- Peptides Or Proteins (AREA)
Abstract
Variance modeling and prediction methods that are useful for assessing whether an amino acid variation at a selected amino acid residue in a protein of interest is likely (or is not likely) to have an effect on the protein (e.g., alter a biological activity of the protein) are described. The methods can be used to generate a structural model or models of all or a part of the protein of interest, assess the quality of the structural model, and evaluate the potential functional consequences of an amino acid variation. The methods achieve these goals by considering certain functional, structural, and phylogenetic features of specific amino acid residues.
Priority Applications (4)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| CA002410726A CA2410726A1 (en) | 2000-06-01 | 2001-05-30 | Structure-based methods for assessing amino acid variances |
| JP2002501137A JP2004501446A (en) | 2000-06-01 | 2001-05-30 | Structure-based methods for assessing amino acid diversity |
| EP01939635A EP1350115A2 (en) | 2000-06-01 | 2001-05-30 | Structure-based methods for assessing amino acid variances |
| AU2001265131A AU2001265131A1 (en) | 2000-06-01 | 2001-05-30 | Structure-based methods for assessing amino acid variances |
Applications Claiming Priority (4)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| US20862800P | 2000-06-01 | 2000-06-01 | |
| US60/208,628 | 2000-06-01 | ||
| US61473500A | 2000-07-12 | 2000-07-12 | |
| US09/614,735 | 2000-07-12 |
Publications (2)
| Publication Number | Publication Date |
|---|---|
| WO2001092990A2 WO2001092990A2 (en) | 2001-12-06 |
| WO2001092990A3 true WO2001092990A3 (en) | 2003-07-31 |
Family
ID=26903348
Family Applications (1)
| Application Number | Title | Priority Date | Filing Date |
|---|---|---|---|
| PCT/US2001/017351 WO2001092990A2 (en) | 2000-06-01 | 2001-05-30 | Structure-based methods for assessing amino acid variances |
Country Status (5)
| Country | Link |
|---|---|
| EP (1) | EP1350115A2 (en) |
| JP (1) | JP2004501446A (en) |
| AU (1) | AU2001265131A1 (en) |
| CA (1) | CA2410726A1 (en) |
| WO (1) | WO2001092990A2 (en) |
Families Citing this family (4)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| US9493753B2 (en) | 2011-03-16 | 2016-11-15 | Amano Enzyme Inc. | Modified α-glucosidase and applications of same |
| CN110223730B (en) * | 2019-06-06 | 2022-09-27 | 河南师范大学 | Prediction method and prediction device for protein and small molecule binding site |
| CN111128300B (en) * | 2019-12-26 | 2023-03-24 | 上海市精神卫生中心（上海市心理咨询培训中心） | Protein interaction influence judgment method based on mutation information |
| CN112257917B (en) * | 2020-10-19 | 2023-05-12 | 北京工商大学 | Time sequence abnormal mode detection method based on entropy characteristics and neural network |
-
2001
- 2001-05-30 JP JP2002501137A patent/JP2004501446A/en active Pending
- 2001-05-30 AU AU2001265131A patent/AU2001265131A1/en not_active Abandoned
- 2001-05-30 WO PCT/US2001/017351 patent/WO2001092990A2/en not_active Application Discontinuation
- 2001-05-30 EP EP01939635A patent/EP1350115A2/en not_active Withdrawn
- 2001-05-30 CA CA002410726A patent/CA2410726A1/en not_active Abandoned
Non-Patent Citations (7)
| Title |
|---|
| CHASMAN DANIEL ET AL: "Predicting the functional consequences of non-synonymous single nucleotide polymorphisms: Structure-based assessment of amino acid variation.", JOURNAL OF MOLECULAR BIOLOGY, vol. 307, no. 2, 2001, pages 683 - 706, XP002212639, ISSN: 0022-2836 * |
| DATABASE BIOSIS [online] BIOSCIENCES INFORMATION SERVICE, PHILADELPHIA, PA, US; 1994, ALTSCHUL STEPHEN F ET AL: "Issues in searching molecular sequence databases.", XP002212660, Database accession no. PREV199497283170 * |
| NATURE GENETICS, vol. 6, no. 2, 1994, pages 119 - 129, ISSN: 1061-4036 * |
| REDDY BOOJALA V B ET AL: "Use of propensities of amino acids to the local structural environments to understand effect of substitution mutations on protein stability.", PROTEIN ENGINEERING, vol. 11, no. 12, December 1998 (1998-12-01), pages 1137 - 1145, XP002212641, ISSN: 0269-2139 * |
| SUNYAEV SHAMIL ET AL: "Prediction of deleterious human alleles.", HUMAN MOLECULAR GENETICS, vol. 10, no. 6, 2001, pages 591 - 597, XP002212640, ISSN: 0964-6906 * |
| SUNYAEV SHAMIL ET AL: "Towards a structural basis of human non-synonymous single nucleotide polymorphisms.", TRENDS IN GENETICS, vol. 16, no. 5, May 2000 (2000-05-01), pages 198 - 200, XP002212759, ISSN: 0168-9525 * |
| WANG ZHEN ET AL: "SNPs, protein structure, and disease.", HUMAN MUTATION, vol. 17, no. 4, 2001, pages 263 - 270, XP001104863, ISSN: 1059-7794 * |
Also Published As
| Publication number | Publication date |
|---|---|
| EP1350115A2 (en) | 2003-10-08 |
| AU2001265131A1 (en) | 2001-12-11 |
| CA2410726A1 (en) | 2001-12-06 |
| JP2004501446A (en) | 2004-01-15 |
| WO2001092990A2 (en) | 2001-12-06 |
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