CA2326134A1 - Method and system for search of implicitly described virtual libraries - Google Patents
Method and system for search of implicitly described virtual libraries Download PDFInfo
- Publication number
- CA2326134A1 CA2326134A1 CA002326134A CA2326134A CA2326134A1 CA 2326134 A1 CA2326134 A1 CA 2326134A1 CA 002326134 A CA002326134 A CA 002326134A CA 2326134 A CA2326134 A CA 2326134A CA 2326134 A1 CA2326134 A1 CA 2326134A1
- Authority
- CA
- Canada
- Prior art keywords
- hypothesis
- compounds
- code
- searching
- fragments
- Prior art date
- Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
- Abandoned
Links
- 238000000034 method Methods 0.000 title claims abstract description 79
- 150000001875 compounds Chemical class 0.000 claims abstract description 119
- 239000000376 reactant Substances 0.000 claims abstract description 74
- 239000012634 fragment Substances 0.000 claims description 105
- 238000006243 chemical reaction Methods 0.000 claims description 83
- 239000000047 product Substances 0.000 claims description 52
- 238000004458 analytical method Methods 0.000 claims description 20
- 230000000694 effects Effects 0.000 claims description 4
- 239000013078 crystal Substances 0.000 claims description 3
- 239000013067 intermediate product Substances 0.000 claims 18
- 239000000126 substance Substances 0.000 abstract description 13
- 150000005829 chemical entities Chemical class 0.000 abstract description 3
- 125000004429 atom Chemical group 0.000 description 45
- 238000010586 diagram Methods 0.000 description 20
- 238000012986 modification Methods 0.000 description 13
- 230000004048 modification Effects 0.000 description 13
- 230000008569 process Effects 0.000 description 12
- 238000012545 processing Methods 0.000 description 10
- 238000002372 labelling Methods 0.000 description 8
- 239000000543 intermediate Substances 0.000 description 7
- 230000008901 benefit Effects 0.000 description 6
- 230000015654 memory Effects 0.000 description 6
- 239000002253 acid Substances 0.000 description 5
- 238000005192 partition Methods 0.000 description 5
- 125000000524 functional group Chemical group 0.000 description 4
- 125000001997 phenyl group Chemical group [H]C1=C([H])C([H])=C(*)C([H])=C1[H] 0.000 description 4
- 230000004044 response Effects 0.000 description 4
- 150000001412 amines Chemical class 0.000 description 3
- 238000013459 approach Methods 0.000 description 3
- 238000005452 bending Methods 0.000 description 3
- 230000000975 bioactive effect Effects 0.000 description 3
- 230000006870 function Effects 0.000 description 3
- 230000003993 interaction Effects 0.000 description 3
- NHCKESBLOMHIIE-IRXDYDNUSA-N Phe-Gly-Phe Chemical compound C([C@H](N)C(=O)NCC(=O)N[C@@H](CC=1C=CC=CC=1)C(O)=O)C1=CC=CC=C1 NHCKESBLOMHIIE-IRXDYDNUSA-N 0.000 description 2
- 150000001413 amino acids Chemical class 0.000 description 2
- 230000015572 biosynthetic process Effects 0.000 description 2
- 238000012512 characterization method Methods 0.000 description 2
- 230000000052 comparative effect Effects 0.000 description 2
- 238000013500 data storage Methods 0.000 description 2
- 238000013461 design Methods 0.000 description 2
- 229940079593 drug Drugs 0.000 description 2
- 239000003814 drug Substances 0.000 description 2
- 238000011156 evaluation Methods 0.000 description 2
- 238000005457 optimization Methods 0.000 description 2
- 230000002093 peripheral effect Effects 0.000 description 2
- 238000002907 substructure search Methods 0.000 description 2
- 238000003786 synthesis reaction Methods 0.000 description 2
- 230000009897 systematic effect Effects 0.000 description 2
- 238000012360 testing method Methods 0.000 description 2
- 230000009466 transformation Effects 0.000 description 2
- 239000005695 Ammonium acetate Substances 0.000 description 1
- CURLTUGMZLYLDI-UHFFFAOYSA-N Carbon dioxide Chemical compound O=C=O CURLTUGMZLYLDI-UHFFFAOYSA-N 0.000 description 1
- OTMSDBZUPAUEDD-UHFFFAOYSA-N Ethane Chemical compound CC OTMSDBZUPAUEDD-UHFFFAOYSA-N 0.000 description 1
- BDAGIHXWWSANSR-UHFFFAOYSA-N Formic acid Chemical compound OC=O BDAGIHXWWSANSR-UHFFFAOYSA-N 0.000 description 1
- LUTSRLYCMSCGCS-BWOMAWGNSA-N [(3s,8r,9s,10r,13s)-10,13-dimethyl-17-oxo-1,2,3,4,7,8,9,11,12,16-decahydrocyclopenta[a]phenanthren-3-yl] acetate Chemical compound C([C@@H]12)C[C@]3(C)C(=O)CC=C3[C@@H]1CC=C1[C@]2(C)CC[C@H](OC(=O)C)C1 LUTSRLYCMSCGCS-BWOMAWGNSA-N 0.000 description 1
- 230000003466 anti-cipated effect Effects 0.000 description 1
- 230000004071 biological effect Effects 0.000 description 1
- 238000006664 bond formation reaction Methods 0.000 description 1
- 238000004422 calculation algorithm Methods 0.000 description 1
- 238000004891 communication Methods 0.000 description 1
- 239000002131 composite material Substances 0.000 description 1
- 238000004590 computer program Methods 0.000 description 1
- 238000007796 conventional method Methods 0.000 description 1
- 230000008878 coupling Effects 0.000 description 1
- 238000010168 coupling process Methods 0.000 description 1
- 238000005859 coupling reaction Methods 0.000 description 1
- 238000000802 evaporation-induced self-assembly Methods 0.000 description 1
- 238000001914 filtration Methods 0.000 description 1
- 235000019253 formic acid Nutrition 0.000 description 1
- 238000002955 isolation Methods 0.000 description 1
- 239000004973 liquid crystal related substance Substances 0.000 description 1
- 230000033001 locomotion Effects 0.000 description 1
- 238000013507 mapping Methods 0.000 description 1
- 239000000463 material Substances 0.000 description 1
- 230000007246 mechanism Effects 0.000 description 1
- 125000000896 monocarboxylic acid group Chemical group 0.000 description 1
- 230000003287 optical effect Effects 0.000 description 1
- 230000008520 organization Effects 0.000 description 1
- 230000002085 persistent effect Effects 0.000 description 1
- 230000000704 physical effect Effects 0.000 description 1
- 239000004297 potassium metabisulphite Substances 0.000 description 1
- 238000005381 potential energy Methods 0.000 description 1
- 108090000765 processed proteins & peptides Proteins 0.000 description 1
- 230000002829 reductive effect Effects 0.000 description 1
- 238000011160 research Methods 0.000 description 1
- LPXPTNMVRIOKMN-UHFFFAOYSA-M sodium nitrite Substances [Na+].[O-]N=O LPXPTNMVRIOKMN-UHFFFAOYSA-M 0.000 description 1
- 239000013589 supplement Substances 0.000 description 1
- 231100000331 toxic Toxicity 0.000 description 1
- 230000002588 toxic effect Effects 0.000 description 1
- 230000000007 visual effect Effects 0.000 description 1
- 238000007704 wet chemistry method Methods 0.000 description 1
Classifications
-
- G—PHYSICS
- G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
- G16C—COMPUTATIONAL CHEMISTRY; CHEMOINFORMATICS; COMPUTATIONAL MATERIALS SCIENCE
- G16C20/00—Chemoinformatics, i.e. ICT specially adapted for the handling of physicochemical or structural data of chemical particles, elements, compounds or mixtures
- G16C20/60—In silico combinatorial chemistry
-
- 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
- G16B35/00—ICT specially adapted for in silico combinatorial libraries of nucleic acids, proteins or peptides
-
- G—PHYSICS
- G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
- G16C—COMPUTATIONAL CHEMISTRY; CHEMOINFORMATICS; COMPUTATIONAL MATERIALS SCIENCE
- G16C20/00—Chemoinformatics, i.e. ICT specially adapted for the handling of physicochemical or structural data of chemical particles, elements, compounds or mixtures
- G16C20/60—In silico combinatorial chemistry
- G16C20/64—Screening of libraries
-
- B—PERFORMING OPERATIONS; TRANSPORTING
- B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
- B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
- B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
- B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
- B01J2219/0068—Means for controlling the apparatus of the process
- B01J2219/00686—Automatic
- B01J2219/00689—Automatic using computers
-
- B—PERFORMING OPERATIONS; TRANSPORTING
- B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
- B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
- B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
- B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
- B01J2219/0068—Means for controlling the apparatus of the process
- B01J2219/007—Simulation or vitual synthesis
Landscapes
- Engineering & Computer Science (AREA)
- Chemical & Material Sciences (AREA)
- Health & Medical Sciences (AREA)
- Life Sciences & Earth Sciences (AREA)
- Bioinformatics & Cheminformatics (AREA)
- General Health & Medical Sciences (AREA)
- Bioinformatics & Computational Biology (AREA)
- Theoretical Computer Science (AREA)
- Computing Systems (AREA)
- Library & Information Science (AREA)
- Crystallography & Structural Chemistry (AREA)
- Medicinal Chemistry (AREA)
- Physics & Mathematics (AREA)
- Biochemistry (AREA)
- Medical Informatics (AREA)
- Spectroscopy & Molecular Physics (AREA)
- Evolutionary Biology (AREA)
- Biotechnology (AREA)
- Molecular Biology (AREA)
- Biophysics (AREA)
- Information Retrieval, Db Structures And Fs Structures Therefor (AREA)
- Investigating Or Analysing Biological Materials (AREA)
- Organic Low-Molecular-Weight Compounds And Preparation Thereof (AREA)
Applications Claiming Priority (5)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| US7975098P | 1998-03-27 | 1998-03-27 | |
| US60/079,750 | 1998-03-27 | ||
| US27299699A | 1999-03-18 | 1999-03-18 | |
| US09/272,996 | 1999-03-18 | ||
| PCT/US1999/006611 WO1999050770A1 (en) | 1998-03-27 | 1999-03-25 | Method and system for search of implicitly described virtual libraries |
Publications (1)
| Publication Number | Publication Date |
|---|---|
| CA2326134A1 true CA2326134A1 (en) | 1999-10-07 |
Family
ID=26762386
Family Applications (1)
| Application Number | Title | Priority Date | Filing Date |
|---|---|---|---|
| CA002326134A Abandoned CA2326134A1 (en) | 1998-03-27 | 1999-03-25 | Method and system for search of implicitly described virtual libraries |
Country Status (9)
| Country | Link |
|---|---|
| EP (1) | EP1066578A1 (pt) |
| JP (1) | JP2004515447A (pt) |
| AU (1) | AU3116199A (pt) |
| BR (1) | BR9909179A (pt) |
| CA (1) | CA2326134A1 (pt) |
| IL (1) | IL138726A0 (pt) |
| NO (1) | NO20004831L (pt) |
| PL (1) | PL343324A1 (pt) |
| WO (1) | WO1999050770A1 (pt) |
Families Citing this family (4)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| US7657378B1 (en) * | 2000-03-30 | 2010-02-02 | Council Of Scientific & Industrial Research | Computer based method for identifying peptides useful as drug targets |
| CA2554979A1 (en) * | 2004-03-05 | 2005-09-29 | Applied Research Systems Ars Holding N.V. | Method for fast substructure searching in non-enumerated chemical libraries |
| EP1628234A1 (en) * | 2004-06-07 | 2006-02-22 | Universita' Degli Studi di Milano-Bicocca | Method of construction and selection of virtual libraries in combinatorial chemistry |
| US10192010B1 (en) | 2016-05-25 | 2019-01-29 | X Development Llc | Simulation of chemical reactions via multiple processing threads |
Family Cites Families (2)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CA2245935C (en) * | 1996-01-26 | 2004-07-20 | David E. Patterson | Method of creating and searching a molecular virtual library using validated molecular structure descriptors |
| EP0818744A3 (en) * | 1996-07-08 | 1998-07-08 | Proteus Molecular Design Limited | Process for selecting candidate drug compounds |
-
1999
- 1999-03-25 IL IL13872699A patent/IL138726A0/xx unknown
- 1999-03-25 WO PCT/US1999/006611 patent/WO1999050770A1/en not_active Application Discontinuation
- 1999-03-25 PL PL99343324A patent/PL343324A1/xx unknown
- 1999-03-25 BR BR9909179-8A patent/BR9909179A/pt not_active Application Discontinuation
- 1999-03-25 JP JP2000541614A patent/JP2004515447A/ja active Pending
- 1999-03-25 EP EP99912899A patent/EP1066578A1/en not_active Withdrawn
- 1999-03-25 CA CA002326134A patent/CA2326134A1/en not_active Abandoned
- 1999-03-25 AU AU31161/99A patent/AU3116199A/en not_active Abandoned
-
2000
- 2000-09-26 NO NO20004831A patent/NO20004831L/no not_active Application Discontinuation
Also Published As
| Publication number | Publication date |
|---|---|
| IL138726A0 (en) | 2001-10-31 |
| PL343324A1 (en) | 2001-08-13 |
| EP1066578A1 (en) | 2001-01-10 |
| WO1999050770A1 (en) | 1999-10-07 |
| AU3116199A (en) | 1999-10-18 |
| NO20004831L (no) | 2000-11-20 |
| BR9909179A (pt) | 2001-10-16 |
| JP2004515447A (ja) | 2004-05-27 |
| NO20004831D0 (no) | 2000-09-26 |
Similar Documents
| Publication | Publication Date | Title |
|---|---|---|
| Cohen | Guidebook on molecular modeling in drug design | |
| Zuckerman et al. | Weighted ensemble simulation: review of methodology, applications, and software | |
| Temelso et al. | ArbAlign: a tool for optimal alignment of arbitrarily ordered isomers using the Kuhn–Munkres algorithm | |
| Lemmen et al. | Computational methods for the structural alignment of molecules | |
| Masek et al. | Molecular shape comparison of angiotensin II receptor antagonists | |
| US20050177280A1 (en) | Methods and systems for discovery of chemical compounds and their syntheses | |
| EP1721268A1 (en) | Method for fast substructure searching in non-enumerated chemical libraries | |
| Gillet et al. | Similarity and dissimilarity methods for processing chemical structure databases | |
| Ivanov et al. | 3DGEN: A system for exhaustive 3D molecular design proceeding from molecular topology | |
| US6253168B1 (en) | Generation of virtual combinatorial libraries of compounds | |
| US6622094B2 (en) | Method for determining relative energies of two or more different molecules | |
| US20040073375A1 (en) | Methods for identifying a molecule that may bind to a target molecule | |
| CA2326134A1 (en) | Method and system for search of implicitly described virtual libraries | |
| WO1998059306A1 (en) | Method and apparatus for conformationally analyzing molecular fragments | |
| JP2004515447A5 (pt) | ||
| US20020077757A1 (en) | Chemistry resource database | |
| Truhlar et al. | Rational Drug Design | |
| Thareja et al. | Computational tools in cheminformatics | |
| US20030087334A1 (en) | Method of flexibly generating diverse reaction chemistries | |
| Swanson | The entrance of informatics into combinatorial chemistry | |
| Glukhovtsev | Recent Developments and Applications of Modern Density Functional Theory. Theoretical and Computational Chemistry; Vol. 4. Edited by JM Seminario. Elsevier: Amsterdam, 1996, xxiv+ 838 pp. List price $409.50. ISBN 0-444-82404-9. | |
| WO2003044219A1 (en) | Method of flexibly generating diverse reaction chemistries | |
| O'Hara-Mays | Genetic Algorithms in Molecular Modeling. Edited by James Devillers. Principles of QSAR and Drug Design, Vol. 1. Academic Press, Harcourt Brace & Company: New York. 1996. 327 pp. ISBN 0-12-213810-4. $55.00. | |
| Ferguson et al. | Design of compound libraries for detecting and pursuing novel small molecule leads | |
| Chines | Computational methodologies for DNA-encoded libraries |
Legal Events
| Date | Code | Title | Description |
|---|---|---|---|
| FZDE | Discontinued |