Welcome to ProMOL

Science is moving at an incredible pace, and novel proteins are discovered and crystallized faster than they can be functionally characterized. Determining the function of a novel protein can be time consuming and expensive. To this end ProMOL software was created to look at structural homology of catalytic sites. Using advanced selection algebra contained in Warren DeLano's PyMOL molecular visualization program, it is possible to define catalytic sites using residue's atom positions from known active sites. This spatially defined matrix made it possible to analyze catalytic sites based on conserved structure instead of relying on sequence homology or entire protein alignments.

ProMOL's Abilities

  • Numerous preset views providing meaningful representations of macromolecules
  • Motif prediction
  • Motif visualization options
  • Motif creation
  • Ligand binding database
  • Display manipulation
  • Easy ray tracing
  • Amino acid reference
  • Electrostatics
  • Links to resources
  • Internal electron density calculation and manipulation
  • External electron density map loading and manipulation
  • Easy atom distance measurement
  • Sequence viewer and different modes
  • Enhanced movie making controls


  • Motif prediction is not perfect
  • Motif creation loses specificity when motifs have duplicate residues
  • RMS values returned for ligand binding database are not very meaningful
  • Complicated system of loading externally generated electron density maps
  • Movie making is still difficult


ProMOL is currently available for download for Windows and Linux users. Click on the link below and follow the instructions included in the readme file in the ProMOL folder.


We would like to recognize everyone who worked on this project. Thank you Brett Hanson, Charlie Westin, Scott Mottarella and Dr. Paul Craig.
The ProMol project is sponsered by the Nation Institute of General Medical Sciences (NIGMS) under Grant number 1R15GM078077-01, the Structural Biology Extensible Visualization Scripting Language.
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