The Resource Efficient search and comparison algorithms for 3D protein binding site retrieval and structure alignment from large-scale databases, by Bin Pang

Efficient search and comparison algorithms for 3D protein binding site retrieval and structure alignment from large-scale databases, by Bin Pang

Label
Efficient search and comparison algorithms for 3D protein binding site retrieval and structure alignment from large-scale databases
Title
Efficient search and comparison algorithms for 3D protein binding site retrieval and structure alignment from large-scale databases
Statement of responsibility
by Bin Pang
Creator
Contributor
Author
Thesis advisor
Subject
Genre
Language
eng
Summary
Finding similar 3D structures is crucial for discovering potential structural, evolutionary, and functional relationships among proteins. As the number of known protein structures has dramatically increased, traditional methods can no longer provide the life science community with the adequate informatics capability needed to conduct large-scale and complex analyses. A suite of high-throughput and accurate protein structure search and comparison methods is essential. To meet the needs of the community, we develop several bioinformatics methods for protein binding site comparison and global structure alignment. First, we developed an efficient protein binding site search that is based on extracting geometric features both locally and globally. The main idea of this work was to capture spatial relationships among landmarks of binding site surfaces and bfuild a vocabulary of visual words to represent the characteristics of the surfaces. A vector model was then used to speed up the search of similar surfaces that share similar visual words with the query interface. Second, we developed an approach for accurate protein binding site comparison. Our algorithm provides an accurate binding site alignment by applying a two-level heuristic process which progressively refines alignment results from coarse surface point level to accurate residue atom level. This setting allowed us to explore different combinations of pairs of corresponding residues, thus improving the alignment quality of the binding site surfaces. Finally, we introduced a parallel algorithm for global protein structure alignment. Specifically, to speed up the time-consuming structure alignment process of protein 3D structures, we designed a parallel protein structure alignment framework to exploit the parallelism of Graphics Processing Units (GPUs). As a general-purpose GPU platform, the framework is capable of parallelizing traditional structure alignment algorithms. Our findings can be applied in various research areas, such as prediction of protein interactions and screening in drug discoveries. The uniqueness of our methods is its ability to manipulate the big data of protein structures by integrating the feature- and alignment-based search and comparison approaches together, thus enabling more efficient and accurate analysis of large-scale protein structures for the research community
Cataloging source
MUU
http://library.link/vocab/creatorDate
1971-
http://library.link/vocab/creatorName
Pang, Bin
Degree
Ph.D.
Dissertation note
Dissertation
Dissertation year
2013.
Government publication
government publication of a state province territory dependency etc
Granting institution
University of Missouri--Columbia
Illustrations
illustrations
Index
no index present
Literary form
non fiction
Nature of contents
  • dictionaries
  • bibliography
  • theses
http://library.link/vocab/relatedWorkOrContributorName
  • Shyu, Chi-Ren
  • Korkin, Dmitry
http://library.link/vocab/subjectName
  • Proteins
  • Protein binding
  • Structural bioinformatics
Label
Efficient search and comparison algorithms for 3D protein binding site retrieval and structure alignment from large-scale databases, by Bin Pang
Instantiates
Publication
Note
  • "May 2013."
  • "A Dissertation presented to the Faculty of Graduate School at the University of Missouri--Columbia In Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy."
  • Dissertation supervisor: Dr. Chi-Ren Shyu
  • Dissertation Co-Supervisor: Dr. Dmitry Korkin
  • Vita
Bibliography note
Includes bibliographical references (pages 98-103)
Carrier category
online resource
Carrier category code
  • cr
Carrier MARC source
rdacarrier.
Content category
text
Content type code
  • txt
Content type MARC source
rdacontent.
Control code
891140769
Extent
1 online resource (x, 104 pages)
Form of item
online
Media category
computer
Media MARC source
rdamedia.
Media type code
  • c
Other physical details
illustrations (chiefly color)
Specific material designation
remote
System control number
(OCoLC)891140769
Label
Efficient search and comparison algorithms for 3D protein binding site retrieval and structure alignment from large-scale databases, by Bin Pang
Publication
Note
  • "May 2013."
  • "A Dissertation presented to the Faculty of Graduate School at the University of Missouri--Columbia In Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy."
  • Dissertation supervisor: Dr. Chi-Ren Shyu
  • Dissertation Co-Supervisor: Dr. Dmitry Korkin
  • Vita
Bibliography note
Includes bibliographical references (pages 98-103)
Carrier category
online resource
Carrier category code
  • cr
Carrier MARC source
rdacarrier.
Content category
text
Content type code
  • txt
Content type MARC source
rdacontent.
Control code
891140769
Extent
1 online resource (x, 104 pages)
Form of item
online
Media category
computer
Media MARC source
rdamedia.
Media type code
  • c
Other physical details
illustrations (chiefly color)
Specific material designation
remote
System control number
(OCoLC)891140769

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