Metal ions are an integral part in both the structural and functional stability of enzymes. The function of an enzyme is exhibited through its active site region, which carries out the reaction for that particular protein. When a metal ion is present in an active site, it not only acts as a structural support for the active site but is often plays a critical role in the functional behavior of the protein. An exhaustive screening for proposed metal ion active sites was performed through online resources including Metal MACiE, Metal PDB, the Catalytic site Atlas and Metal Mine. A total of 103 motifs were generated using ProMol, which is a plugin for the molecular visualization software PyMOL. ProMOL was able to identify these motifs in homologous structures. This new library of enzyme active site motifs was then used to suggest functions for three proteins of unknown function that are found in the Protein Data Bank. An additional functionality was added to ProMOL to enable PyMOL to visualize metal ions and prosthetic groups in enzyme active sites and to calculate the interatomic distances of the active site regions.

Library of Congress Subject Headings

Proteins--Analysis--Data processing; Molecular structure--Data processing; Metal ions--Data processing

Publication Date


Document Type


Student Type


Degree Name

Bioinformatics (MS)


Paul A. Craig

Advisor/Committee Member

Feng Cui

Advisor/Committee Member

Rajendra K. Raj


Physical copy available from RIT's Wallace Library at QH324.2 .K68 2016


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