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WO2003019140A3 - Method for molecular subshape similarity matching - Google Patents

Method for molecular subshape similarity matching Download PDF

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Publication number
WO2003019140A3
WO2003019140A3 PCT/US2002/026844 US0226844W WO03019140A3 WO 2003019140 A3 WO2003019140 A3 WO 2003019140A3 US 0226844 W US0226844 W US 0226844W WO 03019140 A3 WO03019140 A3 WO 03019140A3
Authority
WO
WIPO (PCT)
Prior art keywords
subshape
molecule
query
triangle
target
Prior art date
Application number
PCT/US2002/026844
Other languages
French (fr)
Other versions
WO2003019140A2 (en
Inventor
Santosh Putta
Christian Lemmen
Robert V Stanton
Jeffery Blaney
Leslie Ann Robinson
Original Assignee
Deltagen Res Lab L L C
Priority date (The priority date 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 date listed.)
Filing date
Publication date
Application filed by Deltagen Res Lab L L C filed Critical Deltagen Res Lab L L C
Priority to AU2002329816A priority Critical patent/AU2002329816A1/en
Publication of WO2003019140A2 publication Critical patent/WO2003019140A2/en
Publication of WO2003019140A3 publication Critical patent/WO2003019140A3/en

Links

Classifications

    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/68—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids
    • G01N33/6803—General methods of protein analysis not limited to specific proteins or families of proteins
    • 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
    • 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
    • G16C20/40—Searching chemical structures or physicochemical data

Landscapes

  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Chemical & Material Sciences (AREA)
  • Physics & Mathematics (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Crystallography & Structural Chemistry (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Molecular Biology (AREA)
  • General Health & Medical Sciences (AREA)
  • Theoretical Computer Science (AREA)
  • Biotechnology (AREA)
  • Biophysics (AREA)
  • Hematology (AREA)
  • Evolutionary Biology (AREA)
  • Medical Informatics (AREA)
  • Urology & Nephrology (AREA)
  • Biomedical Technology (AREA)
  • Immunology (AREA)
  • Computing Systems (AREA)
  • Cell Biology (AREA)
  • Microbiology (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Food Science & Technology (AREA)
  • Medicinal Chemistry (AREA)
  • Analytical Chemistry (AREA)
  • Biochemistry (AREA)
  • General Physics & Mathematics (AREA)
  • Pathology (AREA)
  • Image Generation (AREA)
  • Information Retrieval, Db Structures And Fs Structures Therefor (AREA)

Abstract

A database of three-dimensional molecule shapes may be effectively searched for similarity to a query molecule subshape. Triangle matching is first performed between a query subshape triangle representative of a local volume distribution within the query molecule, and a target subshape triangle representative of a local volume distribution within a target molecule of the database. Based upon overlap of the target molecule and query molecule as determined by alignment of matched subshape triangles, shape matching between the aligned query and target molecules is then performed. Comparison of a direction assigned to each vertex of the matched subshape triangles based upon a principal axis of sampled local volume, eliminates unsuitable subshape triangle pairs from consideration prior to the computationally-intensive shape matching step.
PCT/US2002/026844 2001-08-23 2002-08-22 Method for molecular subshape similarity matching WO2003019140A2 (en)

Priority Applications (1)

Application Number Priority Date Filing Date Title
AU2002329816A AU2002329816A1 (en) 2001-08-23 2002-08-22 Method for molecular subshape similarity matching

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US31438001P 2001-08-23 2001-08-23
US60/314,380 2001-08-23

Publications (2)

Publication Number Publication Date
WO2003019140A2 WO2003019140A2 (en) 2003-03-06
WO2003019140A3 true WO2003019140A3 (en) 2004-04-15

Family

ID=23219725

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2002/026844 WO2003019140A2 (en) 2001-08-23 2002-08-22 Method for molecular subshape similarity matching

Country Status (2)

Country Link
AU (1) AU2002329816A1 (en)
WO (1) WO2003019140A2 (en)

Families Citing this family (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN102799779B (en) 2012-07-16 2015-04-22 中山大学 Medicine molecules shape comparing method
WO2014089359A1 (en) * 2012-12-05 2014-06-12 Hudson Robotics, Inc. System for the efficient discovery of new therapeutics drugs
US10515715B1 (en) 2019-06-25 2019-12-24 Colgate-Palmolive Company Systems and methods for evaluating compositions
CN115116553B (en) * 2021-03-19 2024-12-13 本源量子计算科技（合肥）股份有限公司 Molecular parameter configuration method, device, medium and electronic device
WO2023123023A1 (en) * 2021-12-29 2023-07-06 深圳晶泰科技有限公司 Method and device for screening molecules and application thereof

Non-Patent Citations (3)

* Cited by examiner, † Cited by third party
Title
BITTAR ET AL.: "Automatic reconstruction of unstructured 3D data: combining a medial axis and implicit surfaces", COMPUTER GRAPHICS FORUM, vol. 14, no. 3, pages 457 - 468, XP002972808 *
FERMIN ET AL.: "Planar motion detected by randomized triangle matching", PATTERN RECOGNITION LETTERS, vol. 18, no. 8, August 1997 (1997-08-01), pages 741 - 749, XP004103472 *
LEMMEN ET AL.: "FLEXS: a method for fast flexible ligand superposition", J. MEDICINAL CHEMISTRY, vol. 41, 1998, pages 4502 - 4520, XP002241912 *

Also Published As

Publication number Publication date
WO2003019140A2 (en) 2003-03-06
AU2002329816A1 (en) 2003-03-10

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