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PROTEIN STRUCTURE ALIGNMENT USING A GENERALIZED ALIGNMENT MODEL

SUBRAMANIAN, SUCHITHA
http://rave.ohiolink.edu/etdc/view?acc_num=ucin1191966691

Abstract Details

2007, MS, University of Cincinnati, Engineering : Computer Science.
Currently many researchers are working on comparing proteins by aligning their sequences of amino acids. But the structural alignment of proteins is very important. This is because the structure of a protein is believed to be more closely related to function than sequence. There have been a number of tools developed to study three-dimensional protein structure. These include DALI (developed at the European Molecular Biology Laboratory, Cambridge), CHIMERA (developed at the University of California at San Francisco), and CE (developed at the San Diego Supercomputer Center). Most of these tools are vector based or distance based and use the Euclidean distance measure. In this project we use a generalized distance measure, along with powerful pattern-matching heuristics, to understand the functional and structural similarities of proteins whose underlying amino acid sequences may be different. In our method we take the alignments obtained from traditional methods such as CHIMERA and refine them further using a heuristic to minimize the distance between the aligned á-carbon atoms. This method involves formulating a cost function and minimizing it, followed by computation of protein structure alignment and calculating the distance between the two aligned protein structures. Our datasets are taken from the protein structures available in the Protein Data Bank (PDB). The protein structures are represented by their PDB ids. This method uses the coordinates of the á-carbon atoms of the PDB structures as input. Our datasets consist of proteins of various lengths, structural classes and different levels of identities. Our method is compared against popular methods such as DALI, CE, and CHIMERA and we show that it gives better alignment compared to these traditional alignment methods.
Dr. Carla Purdy (Advisor)
78 p.
Computer Science
Protein structure alignment; Euclidean Distance; coordinates of alpha-carbon atoms

Recommended Citations

Citations

  • SUBRAMANIAN, S. (2007). PROTEIN STRUCTURE ALIGNMENT USING A GENERALIZED ALIGNMENT MODEL [Master's thesis, University of Cincinnati]. OhioLINK Electronic Theses and Dissertations Center. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1191966691

    APA Style (7th edition)

  • SUBRAMANIAN, SUCHITHA. PROTEIN STRUCTURE ALIGNMENT USING A GENERALIZED ALIGNMENT MODEL. 2007. University of Cincinnati, Master's thesis. OhioLINK Electronic Theses and Dissertations Center, http://rave.ohiolink.edu/etdc/view?acc_num=ucin1191966691.

    MLA Style (8th edition)

  • SUBRAMANIAN, SUCHITHA. "PROTEIN STRUCTURE ALIGNMENT USING A GENERALIZED ALIGNMENT MODEL." Master's thesis, University of Cincinnati, 2007. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1191966691

    Chicago Manual of Style (17th edition)

ucin1191966691
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© 2007, all rights reserved.
This open access ETD is published by University of Cincinnati and OhioLINK.