CA2391987A1 - Systeme et procede de recherche dans un espace combinatoire - Google Patents

Systeme et procede de recherche dans un espace combinatoire Download PDF

Info

Publication number
CA2391987A1
CA2391987A1 CA002391987A CA2391987A CA2391987A1 CA 2391987 A1 CA2391987 A1 CA 2391987A1 CA 002391987 A CA002391987 A CA 002391987A CA 2391987 A CA2391987 A CA 2391987A CA 2391987 A1 CA2391987 A1 CA 2391987A1
Authority
CA
Canada
Prior art keywords
value
combinations
protein
combination
energy
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
CA002391987A
Other languages
English (en)
Inventor
Amiram Goldblum
Meir Glick
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.)
Yissum Research Development Co of Hebrew University of Jerusalem
Original Assignee
Individual
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 Individual filed Critical Individual
Publication of CA2391987A1 publication Critical patent/CA2391987A1/fr
Abandoned legal-status Critical Current

Links

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
    • 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
    • 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
    • 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

Landscapes

  • Life Sciences & Earth Sciences (AREA)
  • Physics & Mathematics (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Chemical & Material Sciences (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Theoretical Computer Science (AREA)
  • General Health & Medical Sciences (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Biotechnology (AREA)
  • Evolutionary Biology (AREA)
  • Medical Informatics (AREA)
  • Biophysics (AREA)
  • Crystallography & Structural Chemistry (AREA)
  • Biochemistry (AREA)
  • Library & Information Science (AREA)
  • Molecular Biology (AREA)
  • Medicinal Chemistry (AREA)
  • Computing Systems (AREA)
  • Investigating Or Analysing Biological Materials (AREA)
  • Heterocyclic Carbon Compounds Containing A Hetero Ring Having Oxygen Or Sulfur (AREA)
  • Complex Calculations (AREA)

Abstract

L'invention concerne un système et un procédé de recherche dans un espace combinatoire, sans explosion combinatoire. La recherche est effectuée pour diverses combinaisons d'éléments de base, en fonction d'au moins une propriété voulue de combinaison, qui peut être traduite en une mesure quantitative du succès de la recherche. Comme le nombre de variables, et par conséquent le nombre de combinaisons, peut être très grand, on examine de préférence des échantillons de combinaisons. Les éléments de combinaisons qui permettent de maximiser et/ou de favoriser de manière cohérente la mesure quantitative sont ensuite gardés, et les autres éléments sont abandonnés. Le procédé est ensuite répété jusqu'à ce qu'un nombre minimum de combinaisons soit trouvé, celles-ci pouvant être éventuellement évaluées par la suite en fonction d'un paramètre similaire et/ou d'un autre paramètre ou d'une autre caractéristique.
CA002391987A 1999-11-22 2000-11-22 Systeme et procede de recherche dans un espace combinatoire Abandoned CA2391987A1 (fr)

Applications Claiming Priority (5)

Application Number Priority Date Filing Date Title
US16674499P 1999-11-22 1999-11-22
US60/166,744 1999-11-22
US20980600P 2000-06-07 2000-06-07
US60/209,806 2000-06-07
PCT/IL2000/000779 WO2001039098A2 (fr) 1999-11-22 2000-11-22 Systeme et procede de recherche dans un espace combinatoire

Publications (1)

Publication Number Publication Date
CA2391987A1 true CA2391987A1 (fr) 2001-05-31

Family

ID=26862535

Family Applications (1)

Application Number Title Priority Date Filing Date
CA002391987A Abandoned CA2391987A1 (fr) 1999-11-22 2000-11-22 Systeme et procede de recherche dans un espace combinatoire

Country Status (5)

Country Link
EP (1) EP1266337A2 (fr)
JP (1) JP2003524831A (fr)
AU (1) AU780941B2 (fr)
CA (1) CA2391987A1 (fr)
WO (1) WO2001039098A2 (fr)

Cited By (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2014026296A1 (fr) * 2012-08-17 2014-02-20 Zymeworks Inc. Systèmes et procédés pour l'échantillonnage et l'analyse de la dynamique conformationnelle d'un polymère

Families Citing this family (9)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US7315786B2 (en) 1998-10-16 2008-01-01 Xencor Protein design automation for protein libraries
US20020048772A1 (en) 2000-02-10 2002-04-25 Dahiyat Bassil I. Protein design automation for protein libraries
EP1510959A3 (fr) * 2001-08-10 2006-07-26 Xencor, Inc. Automatisation de la conception des protéines pour l'élaboration de bibliothèques de protéines
AU2003252355A1 (en) * 2002-08-01 2004-02-23 Mochida Pharmaceutical Co., Ltd. Novel crystalline tryptase and utilization thereof
TWI413020B (zh) 2008-12-31 2013-10-21 Ind Tech Res Inst 全域極小值的搜尋方法及系統
JP5691575B2 (ja) 2011-02-03 2015-04-01 富士通株式会社 故障解析プログラム，故障解析装置および故障解析方法
LT2951754T (lt) * 2013-01-31 2024-04-25 Codexis, Inc. Biomolekulių identifikavimo naudojant sąveikaujančius komponentus būdai, sistemos ir programinė įranga
CN112649802B (zh) * 2020-12-01 2022-03-22 中国人民解放军海军航空大学 高分辨传感器弱小多目标检测前跟踪方法
JP2022103481A (ja) * 2020-12-28 2022-07-08 富士通株式会社 環状ペプチドの安定構造探索方法、環状ペプチドの安定構造探索プログラム、及び環状ペプチドの安定構造探索装置

Family Cites Families (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
AU751331B2 (en) * 1997-04-11 2002-08-15 California Institute Of Technology Apparatus and method for automated protein design

Cited By (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2014026296A1 (fr) * 2012-08-17 2014-02-20 Zymeworks Inc. Systèmes et procédés pour l'échantillonnage et l'analyse de la dynamique conformationnelle d'un polymère
AU2013302283B2 (en) * 2012-08-17 2015-04-09 Zymeworks Inc. Systems and methods for sampling and analysis of polymer conformational dynamics
US10482991B2 (en) 2012-08-17 2019-11-19 Zymeworks Inc. Systems and methods for sampling and analysis of polymer conformational dynamics

Also Published As

Publication number Publication date
WO2001039098A3 (fr) 2002-09-12
JP2003524831A (ja) 2003-08-19
AU780941B2 (en) 2005-04-28
AU1546901A (en) 2001-06-04
WO2001039098A2 (fr) 2001-05-31
WO2001039098A8 (fr) 2004-04-29
EP1266337A2 (fr) 2002-12-18

Similar Documents

Publication Publication Date Title
Liu et al. MCDOCK: a Monte Carlo simulation approach to the molecular docking problem
Zsoldos et al. eHiTS: a new fast, exhaustive flexible ligand docking system
Halperin et al. Principles of docking: An overview of search algorithms and a guide to scoring functions
Oshiro et al. Flexible ligand docking using a genetic algorithm
De Bakker et al. Ab initio construction of polypeptide fragments: Accuracy of loop decoy discrimination by an all‐atom statistical potential and the AMBER force field with the Generalized Born solvation model
Gehlhaar et al. Molecular recognition of the inhibitor AG-1343 by HIV-1 protease: conformationally flexible docking by evolutionary programming
Xu et al. Hydrogen bonds and salt bridges across protein-protein interfaces.
Meyer et al. Hydrogen bonding and molecular surface shape complementarity as a basis for protein docking
US6230102B1 (en) Computer system and process for identifying a charge distribution which minimizes electrostatic contribution to binding at binding between a ligand and a molecule in a solvent and uses thereof
Amadasi et al. Mapping the energetics of water–protein and water–ligand interactions with the “natural” HINT forcefield: predictive tools for characterizing the roles of water in biomolecules
Friedland et al. A simple model of backbone flexibility improves modeling of side-chain conformational variability
Blaney et al. Computational approaches for combinatorial library design and molecular diversity analysis
Jiang et al. Pharmacophore-based similarity scoring for DOCK
US20070078605A1 (en) Molecular docking technique for screening of combinatorial libraries
JP2002523057A (ja) タンパク質の機能を予測するための方法およびシステム
Mizutani et al. Effective handling of induced‐fit motion in flexible docking
Chen et al. Prediction of protein pairs sharing common active ligands using protein sequence, structure, and ligand similarity
Guterres et al. Ligand-binding-site refinement to generate reliable holo protein structure conformations from apo structures
Verdonk et al. Protein–ligand informatics force field (PLIff): toward a fully knowledge driven “force field” for biomolecular interactions
AU780941B2 (en) System and method for searching a combinatorial space
US20020025535A1 (en) Prioritization of combinatorial library screening
Smith et al. Analysis and optimization of structure-based virtual screening protocols:(3). New methods and old problems in scoring function design
EP1468392B1 (fr) Methode d'identification de sites de liaison utilisant une approche "multi-echelle"
Vengadesan et al. Energy landscape of Met-enkephalin and Leu-enkephalin drawn using mutually orthogonal Latin squares sampling
Glick et al. A novel energy‐based stochastic method for positioning polar protons in protein structures from X‐rays

Legal Events

Date Code Title Description
EEER Examination request
FZDE Discontinued
FZDE Discontinued

Effective date: 20071122