ATE359561T1 - Rechnerverfahren freie energieberechnung für ligandenentwurf verwendend und die voraussage von bindenden zielen - Google Patents

Rechnerverfahren freie energieberechnung für ligandenentwurf verwendend und die voraussage von bindenden zielen

Info

Publication number
ATE359561T1
ATE359561T1 AT98925162T AT98925162T ATE359561T1 AT E359561 T1 ATE359561 T1 AT E359561T1 AT 98925162 T AT98925162 T AT 98925162T AT 98925162 T AT98925162 T AT 98925162T AT E359561 T1 ATE359561 T1 AT E359561T1
Authority
AT
Austria
Prior art keywords
binding
targets
binding targets
optimal
protein
Prior art date
Application number
AT98925162T
Other languages
English (en)
Inventor
Ernesto Freire
Irene Luque
Original Assignee
Univ Johns Hopkins
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 Univ Johns Hopkins filed Critical Univ Johns Hopkins
Application granted granted Critical
Publication of ATE359561T1 publication Critical patent/ATE359561T1/de

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Classifications

    • 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
    • G16B15/30—Drug targeting using structural data; Docking or binding prediction
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K1/00—General methods for the preparation of peptides, i.e. processes for the organic chemical preparation of peptides or proteins of any length
    • 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
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G16B20/30—Detection of binding sites or motifs
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2299/00—Coordinates from 3D structures of peptides, e.g. proteins or enzymes
    • 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
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations

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  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Physics & Mathematics (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Engineering & Computer Science (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • General Health & Medical Sciences (AREA)
  • Biophysics (AREA)
  • Biotechnology (AREA)
  • Medical Informatics (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Theoretical Computer Science (AREA)
  • Evolutionary Biology (AREA)
  • Genetics & Genomics (AREA)
  • Medicinal Chemistry (AREA)
  • Analytical Chemistry (AREA)
  • Crystallography & Structural Chemistry (AREA)
  • Molecular Biology (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Organic Chemistry (AREA)
  • Pharmacology & Pharmacy (AREA)
  • Biochemistry (AREA)
  • Peptides Or Proteins (AREA)
  • Medicines That Contain Protein Lipid Enzymes And Other Medicines (AREA)
  • Steroid Compounds (AREA)
AT98925162T 1997-06-02 1998-06-02 Rechnerverfahren freie energieberechnung für ligandenentwurf verwendend und die voraussage von bindenden zielen ATE359561T1 (de)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US4827497P 1997-06-02 1997-06-02
US6649597P 1997-11-25 1997-11-25

Publications (1)

Publication Number Publication Date
ATE359561T1 true ATE359561T1 (de) 2007-05-15

Family

ID=26725962

Family Applications (1)

Application Number Title Priority Date Filing Date
AT98925162T ATE359561T1 (de) 1997-06-02 1998-06-02 Rechnerverfahren freie energieberechnung für ligandenentwurf verwendend und die voraussage von bindenden zielen

Country Status (7)

Country Link
US (3) US6226603B1 (de)
EP (1) EP1025521B1 (de)
AT (1) ATE359561T1 (de)
CA (1) CA2292697C (de)
DE (1) DE69837555T2 (de)
ES (1) ES2285774T3 (de)
WO (1) WO1998054665A1 (de)

Families Citing this family (57)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US6027711A (en) * 1995-06-07 2000-02-22 Rhomed Incorporated Structurally determined metallo-constructs and applications
AU1760001A (en) * 1999-11-10 2001-06-06 Quest Diagnostics Investments Incorporated Use of computationally derived protein structures of genetic polymorphisms in pharmacogenomics and clinical applications
TW486653B (en) * 2000-03-17 2002-05-11 Hitachi Ltd Chemical material integrated management system and method thereof
AU2001250955A1 (en) * 2000-03-23 2001-10-03 California Institute Of Technology Method and apparatus for predicting ligand binding interactions
CA2346588A1 (en) * 2000-05-08 2001-11-08 Molecular Simulations Inc. Methods and systems for estimating binding affinity
AU2001290731A1 (en) * 2000-09-12 2002-03-26 Johns Hopkins University Structural prediction of allosterism
CN1461411A (zh) * 2000-09-20 2003-12-10 清野祐子 反应检测方法,免疫反应检测方法及其设备
EP1209610A1 (de) * 2000-11-28 2002-05-29 Valentin Capital Management Verfahren und Vorrichtung zur Bestimmung von Ligand/Ziel-Affinitätsdaten
WO2002044990A2 (en) * 2000-11-28 2002-06-06 Valentin Capital Management Apparatus and method for determining affinity data between a target and a ligand
US20050014193A1 (en) * 2003-06-17 2005-01-20 Sharma Shubh D. Identification of target-specific folding sites in peptides and proteins
US7351690B2 (en) * 2000-12-19 2008-04-01 Palatin Technologies, Inc. Knockout identification of target-specific sites in peptides
WO2002054063A1 (en) * 2001-01-04 2002-07-11 Yeda Research And Development Co. Ltd. Database system and method useful for predicting the effect of amino acid substitutions on protein structure and stability
US20030032065A1 (en) * 2001-03-12 2003-02-13 Vince Hilser Ensemble-based strategy for the design of protein pharmaceuticals
EP1373887A1 (de) * 2001-03-12 2004-01-02 Board of Regents, The University of Texas System Strategie auf computerbasis zur zählung von peptid- und protein-konformationsensembles und ligandenaffinitätsanalyse
EP1436316B1 (de) * 2001-04-30 2008-01-23 ZyStor Therapeutics , Inc. Subzelluläres targeting von therapeutischen proteinen
US7560424B2 (en) 2001-04-30 2009-07-14 Zystor Therapeutics, Inc. Targeted therapeutic proteins
US20040005309A1 (en) * 2002-05-29 2004-01-08 Symbiontics, Inc. Targeted therapeutic proteins
US7629309B2 (en) * 2002-05-29 2009-12-08 Zystor Therapeutics, Inc. Targeted therapeutic proteins
WO2002103321A2 (en) * 2001-06-14 2002-12-27 Anadys Pharmaceuticals, Inc. Methods of screening for ligands of target molecules
US7107156B2 (en) * 2001-07-23 2006-09-12 Accelrys Software Inc. Method and apparatus for estimating solvation energies of membrane bound molecules
US20030072761A1 (en) * 2001-10-16 2003-04-17 Lebowitz Jonathan Methods and compositions for targeting proteins across the blood brain barrier
US20090182542A9 (en) * 2001-12-22 2009-07-16 Hilton Jeremy P Hybrid classical-quantum computer architecture for molecular modeling
US6671628B2 (en) * 2002-03-04 2003-12-30 Chemnavigator, Inc. Methods for identifying a molecule that may bind to a target molecule
US20030216867A1 (en) * 2002-03-26 2003-11-20 Campbell Phil G. Methods and systems for molecular modeling
US8273403B2 (en) 2002-05-10 2012-09-25 Bio-Layer Pty Ltd. Generation of surface coating diversity
EP1522037A2 (de) * 2002-05-23 2005-04-13 Board Of Regents The University Of Texas System Vorhersage der signifikanz von snps (einzelnukleotid-polymorphismen) unter verwendung von energieeigenschaften von strukturen auf ensemblebasis
ATE356385T1 (de) * 2002-06-10 2007-03-15 Algonomics N V Verfahren zur vorhersage der bindungsaffinität der mhc-peptid-komplexe
US20040034481A1 (en) * 2002-08-16 2004-02-19 Hurst John R. Methods for identifying a prospective binding site on a target molecule and for characterizing a site on a target molecule
US7660677B2 (en) * 2002-09-03 2010-02-09 Sei-ichi Tanuma Method of designing physiologically active peptide and use thereof
US7610156B2 (en) * 2003-03-31 2009-10-27 Xencor, Inc. Methods for rational pegylation of proteins
US7642340B2 (en) 2003-03-31 2010-01-05 Xencor, Inc. PEGylated TNF-α variant proteins
US7587286B2 (en) * 2003-03-31 2009-09-08 Xencor, Inc. Methods for rational pegylation of proteins
EP1700244A4 (de) * 2003-12-12 2009-07-08 Bio Layer Pty Ltd Verfahren zum entwerfen von oberflächen
DE602005020745D1 (de) * 2004-02-10 2010-06-02 Zystor Therapeutics Inc Saure alpha-glukosidase und fragmente davon
US20070239366A1 (en) * 2004-06-05 2007-10-11 Hilton Jeremy P Hybrid classical-quantum computer architecture for molecular modeling
WO2006002472A1 (en) 2004-07-02 2006-01-12 Bio-Layer Pty Ltd Use of metal complexes
US20060052943A1 (en) * 2004-07-28 2006-03-09 Karthik Ramani Architectures, queries, data stores, and interfaces for proteins and drug molecules
US8117902B2 (en) * 2005-11-03 2012-02-21 University Of Massachusetts Nanopatterned surfaces and related methods for selective adhesion, sensing and separation
EP1966603A4 (de) * 2005-12-30 2009-08-19 Bio Layer Pty Ltd Bindung von molekülen
EP2004678A1 (de) * 2006-03-15 2008-12-24 Csir Modulation der glutaminsynthetaseaktivität
EP1916516A1 (de) * 2006-10-27 2008-04-30 Bayer CropScience AG Methode für die Ermittlung der Intra- und intermolekularen Interaktionen in einer wässrigen Lösung
AU2007322123A1 (en) * 2006-11-13 2008-05-29 Biomarin Pharmaceutical Inc. Methods for treating Pompe disease
US20090006059A1 (en) * 2007-06-27 2009-01-01 Nidhi Arora Systems and methods for mapping binding site volumes in macromolecules
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
US8244504B1 (en) 2007-12-24 2012-08-14 The University Of North Carolina At Charlotte Computer implemented system for quantifying stability and flexibility relationships in macromolecules
US8374828B1 (en) 2007-12-24 2013-02-12 The University Of North Carolina At Charlotte Computer implemented system for protein and drug target design utilizing quantified stability and flexibility relationships to control function
WO2009137721A2 (en) 2008-05-07 2009-11-12 Zystor Therapeutics, Inc. Lysosomal targeting peptides and uses thereof
US8785168B2 (en) 2009-06-17 2014-07-22 Biomarin Pharmaceutical Inc. Formulations for lysosomal enzymes
EA025399B1 (ru) 2010-11-22 2016-12-30 Борис Славинович ФАРБЕР Способ синтеза лечебных и профилактических лекарственных препаратов
WO2013097012A1 (pt) * 2011-12-30 2013-07-04 Embrapa - Empresa Brasileira De Pesquisa Agropecuária Inibidores das enzimas poligalacturonases de fungos fitopatogênicos
CA2868827C (en) * 2012-04-24 2022-05-10 Laboratory Corporation Of America Holdings Methods and systems for identification of a protein binding site
CN103870644B (zh) * 2014-03-11 2016-08-03 中国石油大学(华东) 一种识别MoP催化剂脱氮活性位的方法
EP3289501B1 (de) 2015-05-01 2025-06-18 Schrodinger, LLC Auf physik basierende berechnungsverfahren zur vorhersage von verbindungslöslichkeit
US11756650B2 (en) 2015-11-09 2023-09-12 The University Of British Columbia Systems and methods for predicting misfolded protein epitopes by collective coordinate biasing
US11728011B2 (en) 2019-04-29 2023-08-15 International Business Machines Corporation System and method for molecular design on a quantum computer
IT201900022545A1 (it) 2019-11-29 2021-05-29 Univ Degli Studi Di Bari Aldo Moro Metodo per l’identificazione di regioni di legame specifiche di deidrogenasi fad/nadh-dipendenti di mammiferi e/o di microorganismi patogeni per uomo, altri mammiferi e piante, per il disegno di nuovi farmaci
WO2023172635A1 (en) * 2022-03-08 2023-09-14 Emory University Predictive model for variants associated with drug resistance and theranostic applications thereof

Family Cites Families (6)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5331573A (en) * 1990-12-14 1994-07-19 Balaji Vitukudi N Method of design of compounds that mimic conformational features of selected peptides
DE69329920T2 (de) * 1992-03-27 2001-09-27 Akiko Itai Verfahren zur analyse der struktur von stabilen zusammengesetzten biopolymerligandmolekuelen
US5434796A (en) * 1993-06-30 1995-07-18 Daylight Chemical Information Systems, Inc. Method and apparatus for designing molecules with desired properties by evolving successive populations
US5495423A (en) * 1993-10-25 1996-02-27 Trustees Of Boston University General strategy for vaccine and drug design
US5867402A (en) * 1995-06-23 1999-02-02 The United States Of America As Represented By The Department Of Health And Human Services Computational analysis of nucleic acid information defines binding sites
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

Also Published As

Publication number Publication date
US20050010368A1 (en) 2005-01-13
ES2285774T3 (es) 2007-11-16
US20010000807A1 (en) 2001-05-03
CA2292697A1 (en) 1998-12-03
EP1025521B1 (de) 2007-04-11
EP1025521A1 (de) 2000-08-09
US6226603B1 (en) 2001-05-01
WO1998054665A1 (en) 1998-12-03
EP1025521A4 (de) 2000-11-29
CA2292697C (en) 2006-08-08
DE69837555T2 (de) 2007-12-20
US6772073B2 (en) 2004-08-03
DE69837555D1 (de) 2007-05-24

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