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Utilizing NMR spectroscopy and molec...

Stark, Jaime L.

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Utilizing NMR spectroscopy and molecular docking as tools for the structural determination and functional annotation of proteins.

Record Type:	Language materials, printed : Monograph/item
Title/Author:	Utilizing NMR spectroscopy and molecular docking as tools for the structural determination and functional annotation of proteins./
Author:	Stark, Jaime L.
Description:	307 p.
Notes:	Source: Dissertation Abstracts International, Volume: 74-08(E), Section: B.
Contained By:	Dissertation Abstracts International74-08B(E).
Subject:	Chemistry, General. -
Online resource:	http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=3558795
ISBN:	9781303033759

Utilizing NMR spectroscopy and molecular docking as tools for the structural determination and functional annotation of proteins.
Stark, Jaime L.

Utilizing NMR spectroscopy and molecular docking as tools for the structural determination and functional annotation of proteins. - 307 p.

Source: Dissertation Abstracts International, Volume: 74-08(E), Section: B.

Thesis (Ph.D.)--The University of Nebraska - Lincoln, 2013.

With the completion of the Human Genome Project in 2001 and the subsequent explosion of organisms with sequenced genomes, we are now aware of nearly 28 million proteins. Determining the role of each of these proteins is essential to our understanding of biology and the development of medical advances. Unfortunately, the experimental approaches to determine protein function are too slow to investigate every protein. Bioinformatics approaches, such as sequence and structure homology, have helped to annotate the functions of many similar proteins. However, despite these computational approaches, approximately 40% of proteins still have no known function. Alleviating this deficit will require high-throughput methods that combine experimental and computational approaches.

ISBN: 9781303033759Subjects--Topical Terms:

1021807
Chemistry, General.

Utilizing NMR spectroscopy and molecular docking as tools for the structural determination and functional annotation of proteins.
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020 $a 9781303033759
035 $a (MiAaPQ)AAI3558795
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040 $a MiAaPQ $c MiAaPQ
100 1 $a Stark, Jaime L. $3 2104642
245 1 0 $a Utilizing NMR spectroscopy and molecular docking as tools for the structural determination and functional annotation of proteins.
300 $a 307 p.
500 $a Source: Dissertation Abstracts International, Volume: 74-08(E), Section: B.
500 $a Adviser: Robert Powers.
502 $a Thesis (Ph.D.)--The University of Nebraska - Lincoln, 2013.
520 $a With the completion of the Human Genome Project in 2001 and the subsequent explosion of organisms with sequenced genomes, we are now aware of nearly 28 million proteins. Determining the role of each of these proteins is essential to our understanding of biology and the development of medical advances. Unfortunately, the experimental approaches to determine protein function are too slow to investigate every protein. Bioinformatics approaches, such as sequence and structure homology, have helped to annotate the functions of many similar proteins. However, despite these computational approaches, approximately 40% of proteins still have no known function. Alleviating this deficit will require high-throughput methods that combine experimental and computational approaches.
520 $a Nuclear magnetic resonance (NMR) ligand affinity screens are an experimental approach that can detect protein-ligand interactions, measure a corresponding dissociation constant, and reliably identify the ligand binding site. Correspondingly, molecular docking is a computational tool that can be used predict the location of the binding site and conformation of a compound when bound to a protein using only the structures of both the protein and the compound. Molecular docking provides a rapid way to generate protein-ligand costructures and evaluate numerous compounds in a large chemical library. Together, molecular docking and NMR ligand affinity screens provide valuable information for determining the function of a protein.
520 $a This dissertation describes the high-throughput application of the Functional Annotation Screening Technology by NMR (FAST-NMR), which combines NMR ligand affinity screens, molecular docking, and bioinformatics to help determine the function of 20 previously uncharacterized proteins. Additionally, new tools were developed to utilize 2D 1H, 15N-HSQC (heteronuclear single quantum coherence) chemical shift perturbations (CSPs) and molecular docking to generate consensus binding sites (CSP-Consensus) and protein-ligand costructures (AutoDockFilter). Virtual screening was also successful utilized to identify a potential natural ligand and propose a function for the YndB protein from Bacillus subtilis. Finally, the solution structure of human protein DNAJA1 was determined and its potential role in pancreatic cancer investigated.
590 $a School code: 0138.
650 4 $a Chemistry, General. $3 1021807
650 4 $a Chemistry, Biochemistry. $3 1017722
650 4 $a Chemistry, Analytical. $3 586156
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710 2 $a The University of Nebraska - Lincoln. $b Chemistry. $3 1030646
773 0 $t Dissertation Abstracts International $g 74-08B(E).
790 $a 0138
791 $a Ph.D.
792 $a 2013
793 $a English
856 4 0 $u http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=3558795