WO2002014875A3 - Procede et systeme pour la prediction de sequences d'acides amines compatibles avec une structure tridimensionnelle specifiee - Google Patents

Procede et systeme pour la prediction de sequences d'acides amines compatibles avec une structure tridimensionnelle specifiee Download PDF

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Publication number
WO2002014875A3
WO2002014875A3 PCT/IL2001/000769 IL0100769W WO0214875A3 WO 2002014875 A3 WO2002014875 A3 WO 2002014875A3 IL 0100769 W IL0100769 W IL 0100769W WO 0214875 A3 WO0214875 A3 WO 0214875A3
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WO
WIPO (PCT)
Prior art keywords
amino acid
solvent accessibility
acid sequence
position along
rotamer
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.)
Ceased
Application number
PCT/IL2001/000769
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English (en)
Other versions
WO2002014875A2 (fr
Inventor
Oren M Becker
Maya Topf
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.)
Ramot at Tel Aviv University Ltd
Original Assignee
Ramot at Tel Aviv University Ltd
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
Priority claimed from IL13788600A external-priority patent/IL137886A0/xx
Application filed by Ramot at Tel Aviv University Ltd filed Critical Ramot at Tel Aviv University Ltd
Priority to AU2001280077A priority Critical patent/AU2001280077A1/en
Publication of WO2002014875A2 publication Critical patent/WO2002014875A2/fr
Anticipated expiration legal-status Critical
Publication of WO2002014875A3 publication Critical patent/WO2002014875A3/fr
Ceased legal-status Critical Current

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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 [2D] or three-dimensional [3D] 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
    • G16B15/00—ICT specially adapted for analysing two-dimensional [2D] or three-dimensional [3D] molecular structures, e.g. structural or functional relations or structure alignment
    • G16B15/20—Protein or domain folding

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  • Life Sciences & Earth Sciences (AREA)
  • Physics & Mathematics (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Chemical & Material Sciences (AREA)
  • General Health & Medical Sciences (AREA)
  • Biophysics (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Biotechnology (AREA)
  • Theoretical Computer Science (AREA)
  • Medical Informatics (AREA)
  • Crystallography & Structural Chemistry (AREA)
  • Molecular Biology (AREA)
  • Evolutionary Biology (AREA)
  • Immunology (AREA)
  • Biomedical Technology (AREA)
  • Urology & Nephrology (AREA)
  • Hematology (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Microbiology (AREA)
  • Cell Biology (AREA)
  • Food Science & Technology (AREA)
  • Medicinal Chemistry (AREA)
  • Analytical Chemistry (AREA)
  • Biochemistry (AREA)
  • General Physics & Mathematics (AREA)
  • Pathology (AREA)
  • Peptides Or Proteins (AREA)
  • Management, Administration, Business Operations System, And Electronic Commerce (AREA)

Abstract

Cette invention se rapporte à un procédé pour la prédiction d'une séquence d'acides aminés compatible avec une structure tridimensionnelle (3D) d'une protéine. De façon générale, on construit une représentation virtuelle réduite de cette structure 3D et, pour chaque position le long de ladite représentation, on détermine son accessibilité au solvant. Pour chaque position le long de cette structure, un résidu d'acide aminé est choisi de façon aléatoire dans un groupe prédéfini d'acides aminés ayant une accessibilité au solvant compatible avec l'accessibilité au solvant de la position en question. On réalise sur la protéine envisagée une simulation de Monte-Carlo, dans laquelle un acide aminé dans une position particulière est remplacé séquentiellement par d'autres acides aminés ayant la même accessibilité au solvant, et un résultat énergétique est calculé pour chaque rotamère. Le rotamère ayant le résultat le plus faible pour cette position est ensuite choisi et la simulation de Monte-Carlo est répétée pour chaque position le long de ladite séquence, en vue d'obtenir une séquence d'acides aminés ayant le résultat énergétique total le plus bas. Cette invention concerne également un système informatique, un dispositif mémoire de programmes informatiques lisible par machine et un produit de programme informatique utilisé pour l'exécution de ce procédé.
PCT/IL2001/000769 2000-08-16 2001-08-16 Procede et systeme pour la prediction de sequences d'acides amines compatibles avec une structure tridimensionnelle specifiee Ceased WO2002014875A2 (fr)

Priority Applications (1)

Application Number Priority Date Filing Date Title
AU2001280077A AU2001280077A1 (en) 2000-08-16 2001-08-16 Method and system for predicting amino acid sequence

Applications Claiming Priority (4)

Application Number Priority Date Filing Date Title
IL137886 2000-08-16
IL13788600A IL137886A0 (en) 2000-08-16 2000-08-16 A novel algorithm for de novo protein design
US09/718,425 2000-11-24
US09/718,425 US7751987B1 (en) 2000-08-16 2000-11-24 Method and system for predicting amino acid sequences compatible with a specified three dimensional structure

Publications (2)

Publication Number Publication Date
WO2002014875A2 WO2002014875A2 (fr) 2002-02-21
WO2002014875A3 true WO2002014875A3 (fr) 2003-02-27

Family

ID=26323969

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/IL2001/000769 Ceased WO2002014875A2 (fr) 2000-08-16 2001-08-16 Procede et systeme pour la prediction de sequences d'acides amines compatibles avec une structure tridimensionnelle specifiee

Country Status (2)

Country Link
AU (1) AU2001280077A1 (fr)
WO (1) WO2002014875A2 (fr)

Families Citing this family (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
JP7128346B2 (ja) 2018-09-21 2022-08-30 ディープマインド テクノロジーズ リミテッド 距離マップクロップを組み合わせることによってタンパク質距離マップを決定すること
US12362036B2 (en) 2018-11-30 2025-07-15 Deepmind Technologies Limited Protein structure prediction using geometric attention neural networks
CN114155912B (zh) * 2022-02-09 2022-05-17 北京晶泰科技有限公司 蛋白质的序列设计方法、蛋白质的结构设计方法、装置及电子设备
CN118571306B (zh) * 2024-08-01 2024-11-08 温州大学 一种取代基工程下基态结构预测方法

Citations (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5600571A (en) * 1994-01-18 1997-02-04 The Trustees Of Columbia University In The City Of New York Method for determining protein tertiary structure
WO1998047089A1 (fr) * 1997-04-11 1998-10-22 California Institute Of Technology Dispositif et methode permettant une mise au point informatisee de proteines
WO2001037147A2 (fr) * 1999-11-03 2001-05-25 Algonomics Nv Dispositif et procede permettant la prevision structurelle de sequences d'acides amines

Patent Citations (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5600571A (en) * 1994-01-18 1997-02-04 The Trustees Of Columbia University In The City Of New York Method for determining protein tertiary structure
WO1998047089A1 (fr) * 1997-04-11 1998-10-22 California Institute Of Technology Dispositif et methode permettant une mise au point informatisee de proteines
WO2001037147A2 (fr) * 1999-11-03 2001-05-25 Algonomics Nv Dispositif et procede permettant la prevision structurelle de sequences d'acides amines

Non-Patent Citations (4)

* Cited by examiner, † Cited by third party
Title
DAHIYAT B I ET AL: "De novo protein design: fully automated sequence selection", SCIENCE, AAAS. LANCASTER, PA, US, vol. 278, no. 5335, 3 October 1997 (1997-10-03), pages 82 - 87, XP002188179, ISSN: 0036-8075 *
DAHIYAT B I ET AL: "PROTEIN DESIGN AUTOMATION", PROTEIN SCIENCE, CAMBRIDGE UNIVERSITY PRESS, CAMBRIDGE, GB, vol. 5, no. 5, 1 May 1996 (1996-05-01), pages 895 - 903, XP002073372, ISSN: 0961-8368 *
HERZYK PAWEL ET AL: "A reduced representation of proteins for use in restraint satisfaction calculations.", PROTEINS STRUCTURE FUNCTION AND GENETICS, vol. 17, no. 3, 1993, pages 310 - 324, XP008008288, ISSN: 0887-3585 *
RAHA KAUSHIK ET AL: "Prediction of amino acid sequence from structure.", PROTEIN SCIENCE, vol. 9, no. 6, June 2000 (2000-06-01), pages 1106 - 1119, XP008008198, ISSN: 0961-8368 *

Also Published As

Publication number Publication date
AU2001280077A1 (en) 2002-02-25
WO2002014875A2 (fr) 2002-02-21

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