Title:
METHODS AND SYSTEMS FOR PREDICTING PROTEIN-LIGAND COUPLING SPECIFICITIES
Document Type and Number:
WIPO Patent Application WO2006017181
Kind Code:
A3
Abstract:
The invention provides methods and systems for predicting or evaluating protein-ligand coupling specificities. A pattern recognition model can be trained by selected sequence segments of training proteins which have a specified ligand coupling specificity. Each selected sequence segment is believed to include amino acid residue(s) that may contribute to the ligand coupling specificity of the corresponding training protein. Sequence segments in a protein of interest can be similarly selected and used to query the trained model to determine if the protein of interest has the same ligand coupling specificity as the training proteins. In one embodiment, the pattern recognition model employed is a hidden Markov model which is trained by concatenated cytosolic domains of GPCRs which have interaction preference to a specified class of G proteins. This trained model can be used to evaluate G protein coupling specificity of orphan GPCRs.
Inventors:
SREEKUMAR KODANGATTIL R (US)
HUANG YOUPING (US)
PAUSCH MARK H (US)
GULUKOTA KAMALAKAR (US)
HUANG YOUPING (US)
PAUSCH MARK H (US)
GULUKOTA KAMALAKAR (US)
Application Number:
PCT/US2005/024276
Publication Date:
September 21, 2006
Filing Date:
July 08, 2005
Export Citation:
Assignee:
WYETH CORP (US)
SREEKUMAR KODANGATTIL R (US)
HUANG YOUPING (US)
PAUSCH MARK H (US)
GULUKOTA KAMALAKAR (US)
SREEKUMAR KODANGATTIL R (US)
HUANG YOUPING (US)
PAUSCH MARK H (US)
GULUKOTA KAMALAKAR (US)
International Classes:
C07K14/72; G01N33/566; G16B20/30; G16B30/10; G16B40/20
Other References:
MÖLLER S VILO J CRONING D R: "Prediction of the coupling specificity of G protein coupled receptors to their G proteins", BIOINFORMATICS, OXFORD UNIVERSITY PRESS, OXFORD,, GB, vol. 17, no. SUPPLEMENT 1, 2001, pages S174 - S181, XP002956538, ISSN: 1367-4803
CAO JACK ET AL: "A naive Bayes model to predict coupling between seven transmembrane domain receptors and G-proteins.", BIOINFORMATICS (OXFORD, ENGLAND) 22 JAN 2003, vol. 19, no. 2, 22 January 2003 (2003-01-22), pages 234 - 240, XP002376538, ISSN: 1367-4803
WESS J: "Molecular basis of receptor/G-protein-coupling selectivity.", PHARMACOLOGY & THERAPEUTICS. DEC 1998, vol. 80, no. 3, December 1998 (1998-12-01), pages 231 - 264, XP002376539, ISSN: 0163-7258
BINKOWSKI T A ET AL: "Inferring Functional Relationships of Proteins from Local Sequence and Spatial Surface Patterns", JOURNAL OF MOLECULAR BIOLOGY, LONDON, GB, vol. 332, no. 2, 12 September 2003 (2003-09-12), pages 505 - 526, XP004450113, ISSN: 0022-2836
SREEKUMAR KODANGATTIL R ET AL: "Predicting GPCR-G-protein coupling using hidden Markov models.", BIOINFORMATICS (OXFORD, ENGLAND) 12 DEC 2004, vol. 20, no. 18, 12 December 2004 (2004-12-12), pages 3490 - 3499, XP002376540, ISSN: 1367-4803
CAO JACK ET AL: "A naive Bayes model to predict coupling between seven transmembrane domain receptors and G-proteins.", BIOINFORMATICS (OXFORD, ENGLAND) 22 JAN 2003, vol. 19, no. 2, 22 January 2003 (2003-01-22), pages 234 - 240, XP002376538, ISSN: 1367-4803
WESS J: "Molecular basis of receptor/G-protein-coupling selectivity.", PHARMACOLOGY & THERAPEUTICS. DEC 1998, vol. 80, no. 3, December 1998 (1998-12-01), pages 231 - 264, XP002376539, ISSN: 0163-7258
BINKOWSKI T A ET AL: "Inferring Functional Relationships of Proteins from Local Sequence and Spatial Surface Patterns", JOURNAL OF MOLECULAR BIOLOGY, LONDON, GB, vol. 332, no. 2, 12 September 2003 (2003-09-12), pages 505 - 526, XP004450113, ISSN: 0022-2836
SREEKUMAR KODANGATTIL R ET AL: "Predicting GPCR-G-protein coupling using hidden Markov models.", BIOINFORMATICS (OXFORD, ENGLAND) 12 DEC 2004, vol. 20, no. 18, 12 December 2004 (2004-12-12), pages 3490 - 3499, XP002376540, ISSN: 1367-4803
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