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Title: System and methods for predicting transmembrane domains in membrane proteins and mining the genome for recognizing G-protein coupled receptors

Abstract

The invention provides computer-implemented methods and apparatus implementing a hierarchical protocol using multiscale molecular dynamics and molecular modeling methods to predict the presence of transmembrane regions in proteins, such as G-Protein Coupled Receptors (GPCR), and protein structural models generated according to the protocol. The protocol features a coarse grain sampling method, such as hydrophobicity analysis, to provide a fast and accurate procedure for predicting transmembrane regions. Methods and apparatus of the invention are useful to screen protein or polynucleotide databases for encoded proteins with transmembrane regions, such as GPCRs.

Inventors:
; ; ; ;
Issue Date:
Research Org.:
California Institute of Technology (CalTech), Pasadena, CA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1083211
Patent Number(s):
8370074
Application Number:
12/606,605
Assignee:
California Institute of Technology (Pasadena, CA)
Patent Classifications (CPCs):
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
Resource Type:
Patent
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Trabanino, Rene J, Vaidehi, Nagarajan, Hall, Spencer E, Goddard, William A, and Floriano, Wely. System and methods for predicting transmembrane domains in membrane proteins and mining the genome for recognizing G-protein coupled receptors. United States: N. p., 2013. Web.
Trabanino, Rene J, Vaidehi, Nagarajan, Hall, Spencer E, Goddard, William A, & Floriano, Wely. System and methods for predicting transmembrane domains in membrane proteins and mining the genome for recognizing G-protein coupled receptors. United States.
Trabanino, Rene J, Vaidehi, Nagarajan, Hall, Spencer E, Goddard, William A, and Floriano, Wely. Tue . "System and methods for predicting transmembrane domains in membrane proteins and mining the genome for recognizing G-protein coupled receptors". United States. https://www.osti.gov/servlets/purl/1083211.
@article{osti_1083211,
title = {System and methods for predicting transmembrane domains in membrane proteins and mining the genome for recognizing G-protein coupled receptors},
author = {Trabanino, Rene J and Vaidehi, Nagarajan and Hall, Spencer E and Goddard, William A and Floriano, Wely},
abstractNote = {The invention provides computer-implemented methods and apparatus implementing a hierarchical protocol using multiscale molecular dynamics and molecular modeling methods to predict the presence of transmembrane regions in proteins, such as G-Protein Coupled Receptors (GPCR), and protein structural models generated according to the protocol. The protocol features a coarse grain sampling method, such as hydrophobicity analysis, to provide a fast and accurate procedure for predicting transmembrane regions. Methods and apparatus of the invention are useful to screen protein or polynucleotide databases for encoded proteins with transmembrane regions, such as GPCRs.},
doi = {},
journal = {},
number = ,
volume = ,
place = {United States},
year = {2013},
month = {2}
}

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