DOE Patents title logo U.S. Department of Energy
Office of Scientific and Technical Information

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}
}

Works referenced in this record:

Apparatus and method for automated protein design
patent, July 2001


Methods and apparatus for predicting ligand binding interactions
patent-application, July 2002


A Designed Phenylalanyl-tRNA Synthetase Variant Allows Efficient in Vivo Incorporation of Aryl Ketone Functionality into Proteins
journal, May 2002


Mechanism for antibody catalysis of the oxidation of water by singlet dioxygen
journal, March 2002


Interaction of e. coli outer-membrane protein A with sugars on the receptors of the brain microvascular endothelial cells
journal, December 2002


Analysis of protein transmembrane helical regions by a neural network
journal, April 1994


The hydrophobic moment detects periodicity in protein hydrophobicity.
journal, January 1984


Three-Dimensional Structure of Membrane and Surface Proteins
journal, June 1984


Molecular mechanisms underlying differential odor responses of a mouse olfactory receptor
journal, September 2000


Modelling G-protein-coupled receptors for drug design
journal, November 1999


Structure of the integral membrane domain of the GLP1 receptor
journal, June 1999


Principles of docking: An overview of search algorithms and a guide to scoring functions
journal, May 2002


User-Friendly and Versatile Software for Analysis of Protein Hydrophobicity
journal, August 1998


Ab Initio fold prediction of small helical proteins using distance geometry and knowledge-based scoring functions 1 1Edited by F. Cohen
journal, July 1999


A3-adenosine receptors: Design of selective ligands and therapeutic prospects
journal, January 1995


Conformational preference functions for predicting helices in membrane proteins
journal, February 1993


Applications and statistics for multiple high-scoring segments in molecular sequences.
journal, June 1993


Ca2+-ATPase structure in the E1 and E2 conformations: mechanism, helix–helix and helix–lipid interactions
journal, October 2002


Crystal Structure of Rhodopsin: A G Protein-Coupled Receptor
journal, August 2000


The Prediction of Amphiphilic α-Helices
journal, April 2002


First Principles Predictions of the Structure and Function of G-Protein-Coupled Receptors: Validation for Bovine Rhodopsin
journal, April 2004


Prediction of structure and function of G protein-coupled receptors
journal, September 2002


Virtual Screening for Binding of Phenylalanine Analogues to Phenylalanyl-tRNA Synthetase
journal, December 2002