AU2001250955A1 - Method and apparatus for predicting ligand binding interactions - Google Patents

Method and apparatus for predicting ligand binding interactions

Info

Publication number
AU2001250955A1
AU2001250955A1 AU2001250955A AU5095501A AU2001250955A1 AU 2001250955 A1 AU2001250955 A1 AU 2001250955A1 AU 2001250955 A AU2001250955 A AU 2001250955A AU 5095501 A AU5095501 A AU 5095501A AU 2001250955 A1 AU2001250955 A1 AU 2001250955A1
Authority
AU
Australia
Prior art keywords
ligand binding
binding interactions
predicting ligand
predicting
interactions
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
Application number
AU2001250955A
Inventor
Wely B. Floriano
William A. Goddard Iii
Nagarajan Vaidehi
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
California Institute of Technology CalTech
Original Assignee
California Institute of Technology CalTech
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 California Institute of Technology CalTech filed Critical California Institute of Technology CalTech
Publication of AU2001250955A1 publication Critical patent/AU2001250955A1/en
Abandoned legal-status Critical Current

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
    • G16B15/30—Drug targeting using structural data; Docking or binding prediction
    • 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
    • G16C20/50—Molecular design, e.g. of drugs
    • 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

Landscapes

  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Physics & Mathematics (AREA)
  • Chemical & Material Sciences (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • General Health & Medical Sciences (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Biotechnology (AREA)
  • Molecular Biology (AREA)
  • Biophysics (AREA)
  • Theoretical Computer Science (AREA)
  • Crystallography & Structural Chemistry (AREA)
  • Medicinal Chemistry (AREA)
  • Immunology (AREA)
  • Medical Informatics (AREA)
  • Urology & Nephrology (AREA)
  • Biomedical Technology (AREA)
  • Evolutionary Biology (AREA)
  • Hematology (AREA)
  • Pharmacology & Pharmacy (AREA)
  • Microbiology (AREA)
  • Cell Biology (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Food Science & Technology (AREA)
  • Analytical Chemistry (AREA)
  • Biochemistry (AREA)
  • General Physics & Mathematics (AREA)
  • Pathology (AREA)
  • Computing Systems (AREA)
  • Investigating Or Analysing Biological Materials (AREA)
  • Management, Administration, Business Operations System, And Electronic Commerce (AREA)
AU2001250955A 2000-03-23 2001-03-23 Method and apparatus for predicting ligand binding interactions Abandoned AU2001250955A1 (en)

Applications Claiming Priority (5)

Application Number Priority Date Filing Date Title
US19189500P 2000-03-23 2000-03-23
US60191895 2000-03-23
US21365800P 2000-06-23 2000-06-23
US60213658 2000-06-23
PCT/US2001/009402 WO2001071347A1 (en) 2000-03-23 2001-03-23 Method and apparatus for predicting ligand binding interactions

Publications (1)

Publication Number Publication Date
AU2001250955A1 true AU2001250955A1 (en) 2001-10-03

Family

ID=26887510

Family Applications (1)

Application Number Title Priority Date Filing Date
AU2001250955A Abandoned AU2001250955A1 (en) 2000-03-23 2001-03-23 Method and apparatus for predicting ligand binding interactions

Country Status (4)

Country Link
US (1) US20020099506A1 (en)
EP (1) EP1272839A4 (en)
AU (1) AU2001250955A1 (en)
WO (1) WO2001071347A1 (en)

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US6741937B2 (en) * 2000-05-08 2004-05-25 Accelrys Inc. Methods and systems for estimating binding affinity
US7065453B1 (en) * 2000-06-15 2006-06-20 Accelrys Software, Inc. Molecular docking technique for screening of combinatorial libraries
AU2002356864A1 (en) * 2001-10-29 2003-05-12 Vertex Pharmaceuticals Incorporated Processes for producing optimized pharmacophores
US6671628B2 (en) * 2002-03-04 2003-12-30 Chemnavigator, Inc. Methods for identifying a molecule that may bind to a target molecule
EP1495432A2 (en) * 2002-04-10 2005-01-12 TransTech Pharma Inc. System and method for data analysis, manipulation, and visualization
GB0213186D0 (en) * 2002-06-08 2002-07-17 Univ Dundee Methods
WO2004009614A2 (en) * 2002-07-24 2004-01-29 The Salk Institute For Biological Studies Receptor (sstr4)- selective somatostatin analogs
US20050170433A1 (en) * 2003-04-15 2005-08-04 The Procter & Gamble Company Three dimensional coordinates of melanin-concentrating hormone receptors
WO2004102151A2 (en) * 2003-05-06 2004-11-25 New Century Pharmaceuticals Albumin binding sites for evaluating drug interactions and methods of evaluating or designing drugs based on therir albumin binding properties
US20060009913A1 (en) 2003-07-29 2006-01-12 Trabanino Rene J System and methods for predicting transmembrane domains in membrane proteins and mining the genome for recognizing G-protein coupled receptors
WO2005017805A2 (en) * 2003-08-13 2005-02-24 California Institute Of Technology Systems and methods for predicting the structure and function of multipass transmembrane proteins
EP1684705A4 (en) * 2003-11-03 2008-02-20 New Century Pharmaceuticals Albumin binding sites for evaluating drug interactions and methods of evaluating or designing drugs based on their albumin binding properties
US20050123993A1 (en) * 2003-12-09 2005-06-09 Stephan Brunner Methods of determining ligand residue binding affinity
US7415361B2 (en) * 2003-12-09 2008-08-19 Locus Pharmaceuticals, Inc. Methods and systems for analyzing and determining ligand-residue interaction
CA2600745A1 (en) * 2005-03-03 2006-09-08 The Burnham Institute For Medical Research Screening methods for protein kinase b inhibitors employing virtual docking approaches and compounds and compositions discovered thereby
WO2006110064A2 (en) * 2006-01-20 2006-10-19 Dmitry Gennadievich Tovbin Method for selecting potential medicinal compounds
US20070254307A1 (en) * 2006-04-28 2007-11-01 Verseon Method for Estimation of Location of Active Sites of Biopolymers Based on Virtual Library Screening
US20080014572A1 (en) * 2006-07-13 2008-01-17 Searete Llc, A Limited Liability Corporation Of The State Of Delaware Methods and systems for molecular inhibition
US20090082344A1 (en) * 2006-07-13 2009-03-26 Searete Llc Methods and systems for treating disease
US20080015835A1 (en) * 2006-07-13 2008-01-17 Searete Llc, A Limited Liability Corporation Of The State Of Delaware Methods and systems for treating disease
US20080015833A1 (en) * 2006-07-13 2008-01-17 Searete Llc, A Limited Liability Corporation Of The State Of Delaware Methods and systems for molecular inhibition of protein misfolding
WO2008127136A1 (en) * 2007-04-12 2008-10-23 Dmitry Gennadievich Tovbin Method of determination of protein ligand binding and of the most probable ligand pose in protein binding site
WO2008157729A2 (en) * 2007-06-21 2008-12-24 California Institute Of Technology Methods for predicting three-dimensional structures for alpha helical membrane proteins and their use in design of selective ligands
US7756674B2 (en) * 2007-08-03 2010-07-13 The Trustees Of Columbia University In The City Of New York Methods of calculating differences of binding affinities between congeneric pairs of ligands by way of a displaced solvent functional
US20090124579A1 (en) * 2007-11-09 2009-05-14 University Of South Carolina Systems and Methods For Determination of Compounds for Stimulation or Inhibition of Neocalcification
WO2009086331A1 (en) * 2007-12-20 2009-07-09 Georgia Tech Research Corporation Elucidating ligand-binding information based on protein templates
US20110144966A1 (en) * 2009-11-11 2011-06-16 Goddard Iii William A Methods for prediction of binding poses of a molecule
KR101020933B1 (en) * 2010-02-19 2011-03-09 포항공과대학교 산학협력단 Method for searching ideal protein structures for inhibition of target molecules with simulation from electronic library
US20150051090A1 (en) * 2013-08-19 2015-02-19 D.E. Shaw Research, Llc Methods for in silico screening
CN103500293B (en) * 2013-09-05 2017-07-14 北京工业大学 A kind of screening technique of the nearly natural structure of non-ribosomal protein RNA compounds
ES2774965T3 (en) 2013-09-27 2020-07-23 Codexis Inc Predictive modeling based on structure
DK3418929T3 (en) 2013-09-27 2021-02-01 Codexis Inc AUTOMATED SCREENING OF ENZYME VARIANTS
US20150338423A1 (en) * 2014-05-21 2015-11-26 Sabic Global Technologies B.V. Methods for determining relative binding energy of monomers and methods of using the same
US11435355B2 (en) 2016-02-09 2022-09-06 Albert Einstein College Of Medicine Residue-based pharmacophore method for identifying cognate protein ligands
CN106778059B (en) * 2016-12-19 2019-07-30 浙江工业大学 A kind of group's Advances in protein structure prediction based on Rosetta local enhancement
WO2018213767A1 (en) * 2017-05-19 2018-11-22 Accutar Biotechnology Inc. Computational method for classifying and predicting ligand docking conformations
CN112533941A (en) * 2018-03-05 2021-03-19 斯坦福大学托管董事会 System and method for spatial graph convolution and its application in drug discovery and molecular simulation
KR20210136982A (en) * 2019-01-04 2021-11-17 사이클리카 인코포레이티드 Methods and systems for predicting drug binding using synthetic data
CN112669904B (en) * 2019-10-15 2024-03-01 中国科学院大连化学物理研究所 Screening method for phosphoglycerate kinase and substrate binding mode
IT201900022545A1 (en) 2019-11-29 2021-05-29 Univ Degli Studi Di Bari Aldo Moro METHOD FOR THE IDENTIFICATION OF SPECIFIC BINDING REGIONS OF DEHYDROGENASE FAD / NADH-DEPENDENT MAMMALS AND / OR PATHOGENIC MICROORGANISMS FOR HUMANS, OTHER MAMMALS AND PLANTS, FOR THE DESIGN OF NEW DRUGS
CN116453587B (en) * 2023-06-15 2023-08-29 之江实验室 Task execution method for predicting ligand affinity based on molecular dynamics model

Family Cites Families (6)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
ATE272719T1 (en) * 1993-11-26 2004-08-15 Lawrence B Hendry THE DESIGN OF DRUGS THAT INTERVENTION IN RECEPTOR-LIGAND-DNA INTERACTIONS
US5940307A (en) * 1994-12-14 1999-08-17 The Trustees Of Columbia University In The City Of New York Method for predicting the tendency of a protein to form amphiphilic αβ structure
US5680319A (en) * 1995-05-25 1997-10-21 The Johns Hopkins University School Of Medicine Hierarchical protein folding prediction
US5854992A (en) * 1996-09-26 1998-12-29 President And Fellows Of Harvard College System and method for structure-based drug design that includes accurate prediction of binding free energy
US5873052A (en) * 1996-11-06 1999-02-16 The Perkin-Elmer Corporation Alignment-based similarity scoring methods for quantifying the differences between related biopolymer sequences
CA2292697C (en) * 1997-06-02 2006-08-08 The Johns Hopkins University Computer method utilizing free energy calculations for ligand design and the prediction of binding targets

Also Published As

Publication number Publication date
WO2001071347A8 (en) 2002-02-21
EP1272839A4 (en) 2006-03-01
US20020099506A1 (en) 2002-07-25
WO2001071347A1 (en) 2001-09-27
EP1272839A1 (en) 2003-01-08

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