WO2001037191A3 - Method for manipulating protein or dna sequence data (in order to generate complementary peptide ligands) - Google Patents

Method for manipulating protein or dna sequence data (in order to generate complementary peptide ligands) Download PDF

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Publication number
WO2001037191A3
WO2001037191A3 PCT/GB2000/004418 GB0004418W WO0137191A3 WO 2001037191 A3 WO2001037191 A3 WO 2001037191A3 GB 0004418 W GB0004418 W GB 0004418W WO 0137191 A3 WO0137191 A3 WO 0137191A3
Authority
WO
WIPO (PCT)
Prior art keywords
regions
procedure
sequence data
order
dna sequence
Prior art date
Application number
PCT/GB2000/004418
Other languages
French (fr)
Other versions
WO2001037191A2 (en
Inventor
Gareth Wyn Roberts
Jonathan Richard Heal
Original Assignee
Proteom Ltd
Gareth Wyn Roberts
Jonathan Richard Heal
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 Proteom Ltd, Gareth Wyn Roberts, Jonathan Richard Heal filed Critical Proteom Ltd
Priority to EP00979742A priority Critical patent/EP1230615A2/en
Priority to AU17134/01A priority patent/AU1713401A/en
Publication of WO2001037191A2 publication Critical patent/WO2001037191A2/en
Publication of WO2001037191A3 publication Critical patent/WO2001037191A3/en

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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
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • 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
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • G16B30/10—Sequence alignment; Homology search
    • 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

Abstract

This method enables computational analysis and manipulation of DNA and protein sequence data such as is found in large public databases. The method allows systematic searches of such data to identify portion of sequences which code for key intermolecular surfaces or regions of specific protein targets. In a first example, two amino acid sequences are input (steps 1,2) to an iterative procedure (steps 4-6). A frame size is selected, in terms of a number of sequence elements. The procedure then compares pairs of frames, one from each sequence, to identify intramolecular and intermolecular regions on the basis of relationships between amino acids according to a predetermined coding scheme. The probability of existence of each region within the coding scheme is then evaluated and those regions for which the probability is greater than a predetermined threshold are discarded. The procedure outputs the remaining regions.
PCT/GB2000/004418 1999-11-19 2000-11-20 Method for manipulating protein or dna sequence data (in order to generate complementary peptide ligands) WO2001037191A2 (en)

Priority Applications (2)

Application Number Priority Date Filing Date Title
EP00979742A EP1230615A2 (en) 1999-11-19 2000-11-20 Method for manipulating protein or dna sequence data in order to generate complementary peptide ligands
AU17134/01A AU1713401A (en) 1999-11-19 2000-11-20 Method for manipulating protein or dna sequence data (in order to generate complementary peptide ligands)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
GB9927485.4 1999-11-19
GB9927485A GB2356401A (en) 1999-11-19 1999-11-19 Method for manipulating protein or DNA sequence data

Publications (2)

Publication Number Publication Date
WO2001037191A2 WO2001037191A2 (en) 2001-05-25
WO2001037191A3 true WO2001037191A3 (en) 2002-03-21

Family

ID=10864860

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/GB2000/004418 WO2001037191A2 (en) 1999-11-19 2000-11-20 Method for manipulating protein or dna sequence data (in order to generate complementary peptide ligands)

Country Status (5)

Country Link
US (1) US6721663B1 (en)
EP (1) EP1230615A2 (en)
AU (1) AU1713401A (en)
GB (1) GB2356401A (en)
WO (1) WO2001037191A2 (en)

Families Citing this family (7)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
GB0119890D0 (en) * 2001-08-15 2001-10-10 Proteom Ltd Apparatus and method for predicting rules of protein sequence interactions
CN1826137A (en) * 2002-11-01 2006-08-30 博伊斯镇国家研究医院 Inducible ligand for alpha1beta1 integrin and uses
AU2003902621A0 (en) * 2003-05-27 2003-06-12 Commonwealth Scientific And Industrial Research Organisation Ecdysone receiptor ligand-binding domain structure
WO2007035406A1 (en) * 2005-09-16 2007-03-29 Orthologic Corp. Antibodies to complementary peptides of thrombin or portions thereof
US9268903B2 (en) 2010-07-06 2016-02-23 Life Technologies Corporation Systems and methods for sequence data alignment quality assessment
US10327812B2 (en) 2015-11-04 2019-06-25 Rainbow Medical Ltd. Pericardial access device
US10667842B2 (en) 2017-11-24 2020-06-02 Rainbow Medical Ltd. Pericardial needle mechanism

Citations (6)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5081584A (en) * 1989-03-13 1992-01-14 United States Of America Computer-assisted design of anti-peptides based on the amino acid sequence of a target peptide
US5212072A (en) * 1985-03-01 1993-05-18 Board Of Regents, The University Of Texas System Polypeptides complementary to peptides or proteins having an amino acid sequence or nucleotide coding sequence at least partially known and methods of design therefor
US5523208A (en) * 1994-11-30 1996-06-04 The Board Of Trustees Of The University Of Kentucky Method to discover genetic coding regions for complementary interacting proteins by scanning DNA sequence data banks
WO1998037242A1 (en) * 1997-02-24 1998-08-27 Tm Technologies, Inc. Process for selecting anti-sense oligonucleotides
WO1999042621A2 (en) * 1998-02-21 1999-08-26 Tm Technologies, Inc. Methods for identifying or characterising a site based on the thermodynamic properties of nucleic acids
WO1999055911A1 (en) * 1998-04-24 1999-11-04 Fang Fang Identifying peptide ligands of target proteins with target complementary library technology (tclt)

Family Cites Families (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5884230A (en) * 1993-04-28 1999-03-16 Immunex Corporation Method and system for protein modeling

Patent Citations (6)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5212072A (en) * 1985-03-01 1993-05-18 Board Of Regents, The University Of Texas System Polypeptides complementary to peptides or proteins having an amino acid sequence or nucleotide coding sequence at least partially known and methods of design therefor
US5081584A (en) * 1989-03-13 1992-01-14 United States Of America Computer-assisted design of anti-peptides based on the amino acid sequence of a target peptide
US5523208A (en) * 1994-11-30 1996-06-04 The Board Of Trustees Of The University Of Kentucky Method to discover genetic coding regions for complementary interacting proteins by scanning DNA sequence data banks
WO1998037242A1 (en) * 1997-02-24 1998-08-27 Tm Technologies, Inc. Process for selecting anti-sense oligonucleotides
WO1999042621A2 (en) * 1998-02-21 1999-08-26 Tm Technologies, Inc. Methods for identifying or characterising a site based on the thermodynamic properties of nucleic acids
WO1999055911A1 (en) * 1998-04-24 1999-11-04 Fang Fang Identifying peptide ligands of target proteins with target complementary library technology (tclt)

Non-Patent Citations (1)

* Cited by examiner, † Cited by third party
Title
BARANYI L ET AL: "THE ANTISENSE HOMOLOGY BOX: A NEW MOTIF WITHIN PROTEINS THAT ENCODES BIOLOGICALLY ACTIVE PEPTIDES", NATURE MEDICINE,NATURE PUBLISHING, CO,US, vol. 1, no. 9, September 1995 (1995-09-01), pages 894 - 901, XP000984564, ISSN: 1078-8956 *

Also Published As

Publication number Publication date
US6721663B1 (en) 2004-04-13
AU1713401A (en) 2001-05-30
WO2001037191A2 (en) 2001-05-25
GB9927485D0 (en) 2000-01-19
EP1230615A2 (en) 2002-08-14
GB2356401A (en) 2001-05-23

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