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

Links

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

Landscapes

  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Physics & Mathematics (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Biophysics (AREA)
  • General Health & Medical Sciences (AREA)
  • Biotechnology (AREA)
  • Medical Informatics (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Theoretical Computer Science (AREA)
  • Evolutionary Biology (AREA)
  • Medicinal Chemistry (AREA)
  • Genetics & Genomics (AREA)
  • Analytical Chemistry (AREA)
  • Molecular Biology (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Crystallography & Structural Chemistry (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
WO2001035316A2 (en) * 1999-11-10 2001-05-17 Structural Bioinformatics, Inc. Computationally derived protein structures in pharmacogenomics
TW486653B (en) * 2000-03-17 2002-05-11 Hitachi Ltd Chemical material integrated management system and method thereof
EP1272839A4 (de) * 2000-03-23 2006-03-01 California Inst Of Techn Verfahren und vorrichtung zum vorhersagen von interaktionen bei der ligandenbindung
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
EP1319949A4 (de) * 2000-09-20 2005-06-01 Yuko Seino Verfahren zum nachweis von reaktionen oder immunreaktionen und vorrichtung
EP1209610A1 (de) * 2000-11-28 2002-05-29 Valentin Capital Management Verfahren und Vorrichtung zur Bestimmung von Ligand/Ziel-Affinitätsdaten
AU2002231706A1 (en) * 2000-11-28 2002-06-11 Clairbio 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
WO2002073373A2 (en) * 2001-03-12 2002-09-19 Board Of Regents, University Of Texas System Ensemble-based strategy for the design of protein pharmaceuticals
CA2440443A1 (en) * 2001-03-12 2002-09-19 Robert O. Fox Computer-based strategy for peptide and protein conformational ensemble enumeration and ligand affinity analysis
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
US7560424B2 (en) 2001-04-30 2009-07-14 Zystor Therapeutics, Inc. Targeted therapeutic proteins
AU2002256423B2 (en) * 2001-04-30 2008-07-24 Zystor Therapeutics, Inc. Subcellular targeting of therapeutic proteins
JP2004537047A (ja) * 2001-06-14 2004-12-09 アナディーズ　ファーマスーティカルズ，アイエヌシー． 標的分子のリガンドをスクリーニングする方法
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
EP1534755B1 (de) 2002-05-10 2011-10-12 Bio-Layer Pty Limited Erzeugung von oberflächenbeschichtungsdivergenz
AU2003241565A1 (en) * 2002-05-23 2003-12-12 Board Of Regents, The University Of Texas System Predicting the significance of single nucleotide polymorphisms (snps) using ensemble-based structural energetics
US7702465B2 (en) * 2002-06-10 2010-04-20 Algonomics N.V. Method, computing routine, device for predicting properties of MHC/peptide complexes, and data and peptides produced therefrom
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
WO2004022737A1 (ja) * 2002-09-03 2004-03-18 Sei-Ichi Tanuma 生理活性ペプチドの設計法及びその用途
US7642340B2 (en) 2003-03-31 2010-01-05 Xencor, Inc. PEGylated TNF-α variant proteins
US7610156B2 (en) * 2003-03-31 2009-10-27 Xencor, Inc. Methods for rational pegylation of proteins
WO2004089421A2 (en) * 2003-03-31 2004-10-21 Xencor, Inc Methods for rational pegylation of proteins
WO2005057462A1 (en) * 2003-12-12 2005-06-23 Bio-Layer Pty Limited A method for designing surfaces
JP4914224B2 (ja) * 2004-02-10 2012-04-11 バイオマリン ファーマシューティカル インコーポレイテッド 酸性αグルコシダーゼおよびそのフラグメント
US20070239366A1 (en) * 2004-06-05 2007-10-11 Hilton Jeremy P Hybrid classical-quantum computer architecture for molecular modeling
US8168445B2 (en) 2004-07-02 2012-05-01 Bio-Layer Pty Limited 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
WO2007076580A1 (en) * 2005-12-30 2007-07-12 Bio-Layer Pty Limited Binding of molecules
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
EP2099523A2 (de) * 2006-11-13 2009-09-16 ZyStor Therapeutics , Inc. Verfahren zur behandlung von pompe-krankheit
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
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
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
US20110223147A1 (en) 2008-05-07 2011-09-15 Zystor Therapeutics, Inc. Lysosomal targeting peptides and uses thereof
ES2758827T3 (es) 2009-06-17 2020-05-06 Biomarin Pharm Inc Formulaciones para enzimas lisosómicas
WO2012070968A1 (ru) 2010-11-22 2012-05-31 Farber Boris Slavinovich Способ молекулярного дизайна и синтеза лечебных и профилактических лекарст- венных препаратов
WO2013097012A1 (pt) * 2011-12-30 2013-07-04 Embrapa - Empresa Brasileira De Pesquisa Agropecuária Inibidores das enzimas poligalacturonases de fungos fitopatogênicos
US20130280238A1 (en) * 2012-04-24 2013-10-24 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
DK3289501T3 (da) 2015-05-01 2025-09-15 Schrodinger Llc Fysikbaserede beregningsmetoder til forudsigelse af en forbindelses opløselighed
CN108475298A (zh) * 2015-11-09 2018-08-31 英属哥伦比亚大学 通过集体坐标偏置预测错误折叠的蛋白质表位的系统和方法
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
EP0633534B1 (de) * 1992-03-27 2001-02-07 ITAI, Akiko 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
CA2292697C (en) 2006-08-08
US6226603B1 (en) 2001-05-01
US20010000807A1 (en) 2001-05-03
CA2292697A1 (en) 1998-12-03
DE69837555D1 (de) 2007-05-24
US20050010368A1 (en) 2005-01-13
DE69837555T2 (de) 2007-12-20
EP1025521A4 (de) 2000-11-29
US6772073B2 (en) 2004-08-03
WO1998054665A1 (en) 1998-12-03
ES2285774T3 (es) 2007-11-16
EP1025521B1 (de) 2007-04-11
EP1025521A1 (de) 2000-08-09

Similar Documents

Publication Publication Date Title
ATE359561T1 (de) Rechnerverfahren freie energieberechnung für ligandenentwurf verwendend und die voraussage von bindenden zielen
Gygi et al. Evaluation of two-dimensional gel electrophoresis-based proteome analysis technology
Kritzer et al. β-Peptides as inhibitors of protein–protein interactions
Mei et al. A new set of amino acid descriptors and its application in peptide QSARs
Chong et al. Interaction with the surrounding water plays a key role in determining the aggregation propensity of proteins
Kohagen et al. Calcium binding to calmodulin by molecular dynamics with effective polarization
Massova et al. Combined molecular mechanical and continuum solvent approach (MM-PBSA/GBSA) to predict ligand binding
Yang et al. A two-step binding mechanism for the self-binding peptide recognition of target domains
Li et al. Energy landscape views for interplays among folding, binding, and allostery of calmodulin domains
Paterová et al. Reversal of the Hofmeister series: specific ion effects on peptides
Kong et al. Signaling pathways of PDZ2 domain: a molecular dynamics interaction correlation analysis
Fiol et al. Formation of protein kinase recognition sites by covalent modification of the substrate. Molecular mechanism for the synergistic action of casein kinase II and glycogen synthase kinase 3.
Geertz et al. Massively parallel measurements of molecular interaction kinetics on a microfluidic platform
Whitten et al. Cardiac myosin-binding protein C decorates F-actin: implications for cardiac function
Malleshappa Gowder et al. Prediction and analysis of surface hydrophobic residues in tertiary structure of proteins
Weintraub Release of discrete subunits after nuclease and trypsin digestion of chromatin.
Washburn Utilisation of proteomics datasets generated via multidimensional protein identification technology (MudPIT)
Spicer et al. N-capping motifs promote interaction of amphipathic helical peptides with hydrophobic surfaces and drastically alter hydrophobicity values of individual amino acids
Chen et al. Rational design of YAP WW1 domain‐binding peptides to target TGFβ/BMP/Smad–YAP interaction in heterotopic ossification
Herrmann et al. Microheterogeneity of microtubule-associated proteins, MAP-1 and MAP-2, and differential phosphorylation of individual subcomponents.
Cox et al. Global analysis of SUMO-binding proteins identifies SUMOylation as a key regulator of the INO80 chromatin remodeling complex
Kroiss et al. Unbiased discovery of dynamic peptide‐ATP complexes
Jing et al. Rational design of angiotensin‐I‐converting enzyme inhibitory peptides by integrating in silico modeling and an in vitro assay
Caron et al. Proteomic map and database of lymphoblastoid proteins
Collins et al. Robust enrichment of phosphorylated species in complex mixtures by sequential protein and peptide metal-affinity chromatography and analysis by tandem mass spectrometry

Legal Events

Date Code Title Description
RER Ceased as to paragraph 5 lit. 3 law introducing patent treaties