Recognition of metal ions using ProMOL to improve protein function assignation (777.1)

Abstract

ProMOL is a plugin for PyMOL that utilizes the 3D visualization and measurement capacities of PyMOL to predict enzyme function by aligning query structures with a collection of annotated active sites found in our motif template library. The focus of this initiative is a response to the >3000 structures in the Protein Data Bank that are labeled as having “unknown function”. ProMOL undergoes constant revision and development from the various team members from RIT and Dowling College. The motif capabilities of ProMOL have been expanded to include metal ions and prosthetic groups that are found in enzyme active sites, as nearly 40% of all the PDB structures contain at least one metal ion. This is biologically significant as metal ions such as Mn, Zn, Ca and Fe, play a vital role in both the structure and function of many different proteins. The addition of metal ion recognition to ProMOL/PyMOL promises to lead us to better function assignments to this collection of protein structures. There are current plans to launch a database with specific information pertaining to the metal ion binding sites and 3D visualization of motifs with metal ions. This work has been supported in part by National Institute of General Medical Sciences 2R15GM078077‐02, 3R15GM078077‐02S1.Grant Funding Source: Supported by NIGMS 2R15GM078077‐02, 3R15GM078077‐02S1