The ability of structural genomics consortia to determine protein structures more quickly than the proteins can be functionally annotated by conventional experimental means has generated a significant bottleneck that inhibits the progress of certain areas of biological and medical research. This issue is currently being addressed in part by the development of computational resources, which can suggest functions for proteins of interest based on their structure. ProMOL is such a resource, and the method that it employs is based on detecting, in structures of unknown function, motifs of known function from a template library. Access to ProMOL results has been limited, due to a number of factors including the computational requirements for generating novel results and the format in which results have been stored. In this project, a remote results database that can be shared by the ProMOL user community has been implemented and integrated into the ProMOL client program. The introduction of database features addresses several of the drawbacks ProMOL previously had, especially related to efficiency, redundant computations, and the ability to maximize the potential utility of accumulated analysis results. Using the database has no effect on performance in the worst case scenario, and in the best case scenario it decreases runtime by >99%. Analyses of accumulated results in the database facilitate better quantification of the accuracy and performance of ProMOL, and suggest ways to improve the program. Finally, the database constitutes a novel resource with a variety of potential avenues of investigation that have not been possible previously.

Library of Congress Subject Headings

Proteins--Analysis--Data processing; Proteins--Databases; Genomics--Data processing

Publication Date


Document Type


Student Type


Degree Name

Bioinformatics (MS)

Department, Program, or Center

Thomas H. Gosnell School of Life Sciences (COS)


Paul A. Craig

Advisor/Committee Member

Michael V. Osier

Advisor/Committee Member

Gregory A. Babbitt


Physical copy available from RIT's Wallace Library at QH324.2 .G74 2016


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