Mathematical methods for protein structural motif recognition

In this thesis, two algorithms for protein structural motif recognition are presented. A program is described which successfully recognizes the occurrence of the right-handed parallel 8-helix fold from protein sequence data alone. When run on sequences of unknown structure the program identifies the fold in a significant number of microbial outer membrane and cell-surface proteins implicated in infectious disease. A search algorithm is introduced for unsupervised discovery of protein sequence patterns that are significantly correlated with structural motifs. The algorithm identifies known, biologically relevant patterns as well as several potentially novel motifs. It is hoped that both algorithms may contribute to a better understanding of the connection between protein sequence and structure.

Department dc:contributor.department

Massachusetts Institute of Technology. Dept. of Mathematics.

Grantor dc:publisher

Massachusetts Institute of Technology

Year dc:date.issued

2001

Author dc:creator

• Bradley, Philip H. (Philip Harlan), 1973-

Advisor dc:contributor.advisor

• Bonnie Berger.

• Mathematics.

Statement dc:rights

• M.I.T. theses are protected by copyright. They may be viewed from this source for any purpose, but reproduction or distribution in any format is prohibited without written permission. See provided URL for inquiries about permission.

Licence dc:rights.uri

• http://dspace.mit.edu/handle/1721.1/7582

Language dc:language.iso

eng

Handle dc:identifier.uri

http://hdl.handle.net/1721.1/8641

OAI identifier oai:identifier

oai:dspace.mit.edu:1721.1/8641