Youping P Huang

US Patent:

20100293118, Nov 18, 2010

Filed:

May 26, 2010

Appl. No.:

12/787725

Inventors:

Youping Huang - Plainsboro NJ, US
Mark H. Pausch - Rocky Hill NJ, US
Kamalakar Gulukota - Hyderabad, IN

Assignee:

Wyeth LLC - Madison NJ

International Classification:

G06F 15/18
G06G 7/48
C12N 5/02
G06N 5/02

US Classification:

706 12, 703 11, 435375, 706 48

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.

US Patent:

20060008831, Jan 12, 2006

Filed:

Jul 8, 2005

Appl. No.:

11/176621

Inventors:

Youping Huang - Plainsboro NJ, US
Mark Pausch - Rocky Hill NJ, US
Kamalakar Gulukota - Hyderabad, IN

International Classification:

C12Q 1/68
G01N 33/53
G06F 19/00

US Classification:

435006000, 435007100, 702019000

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.