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Abstract

Grant Number:	1R41GM067439-01
PI Name:	OSTLUND, NEIL S.
PI Email:	ostlund@hyper.com
PI Title:	PRESIDENT AND CEO, HYPERCUBE INC.
Project Title:	Evolutionary Analysis of Proteins using HyperChem

Abstract: DESCRIPTION (provided by applicant): Various "higher order" phenomena are displayed by protein sequences as they divergently evolve under functional constraints. These include correlated replacement at different sites in the sequence, changing patterns of mutation at different sites and in different parts of the evolutionary tree, and convergent and parallel sequence evolution. These phenomena carry information that has biomedical and scientific significance, including information about protein folding, protein behavior, protein-protein interactions, and protein function. Those seeking to interpret the global proteome would find valuable a tool that permits the visualization of these evolutionary phenomena within the context of a three dimensional structure of the protein. This proposal seeks funding to establish a technology transfer collaboration between the Foundation for Scientific Inquiry, a nonprofit organization that develops interpretive proteomics strategies as part of its research and education missions, and HyperCube, a for-profit concern that distributes HyperChem, a computer software package that analyzes chemical structures using quantum mechanics, molecular modeling, and graphics visualization. The product of this collaboration will be an enhanced version of HyperChem that places residues displaying interesting higher order phenomena on to a three dimensional model of the "consensus fold" of the protein family, and then displays this model in a graphic user interface for a user to analyze. The advantage of this partnership is that the Foundation already has developed many of the scientific concepts, and validated these in case studies, while HyperChem already incorporates many of the basic program modules that enable visualization. The partnership will also take advantage of HyperChem's wide market within chemistry, biochemistry, and molecular biology departments across the United States. This educational market is not reached effectively by the product that the Foundation has already developed with EraGen Biosciences. This will also, however, be a new direction for HyperChem, and open a market for HyperCube's product for non-educational customers, including pharmaceutical and biotechnology companies.

Thesaurus Terms:
biochemical evolution, chemical model, computer assisted sequence analysis, computer system design /evaluation, protein folding, protein sequence, proteomics, quantum chemistry, three dimensional imaging /topography
chemical structure, computer human interaction, computer program /software, computer simulation, protein structure function, structural biology

Institution:	HYPERCUBE
	1115 NW 4TH ST
	GAINESVILLE, FL 32601
Fiscal Year:	2003
Department:
Project Start:	01-JUN-2003
Project End:	31-MAY-2004
ICD:	NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES
IRG:	ZRG1

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