Structural Alignment with PyMOL and ProMOL


Teaching: 30 min
Exercises: 120 min
  • How are PyMOL and ProMOL used to align active sites?

  • Students will describe typical characteristics of an enzyme active site. Students will understand and be able to explain the term motif and apply it to enzyme active sites.

  • Students will be able to query structures of unknown function against a library of enzyme active site motif templates.

  • Students will distinguish between good alignments and poor alignments of unknown versus known proteins based on Levenshtein distance (a measure of the similarity between two data sets), RMSD values (a measure of the differences between values), and visual alignments.

  • Students will propose a function for proteins of unknown function and develop plans for testing their hypothesis in silico and in vitro.

ProMOL ProMOL is a plug-in to the PyMOL molecular graphics environment that enables uses to query any protein structure against a library of more than 1000 annotated enzyme active sites. Results include quantitative measures of the alignment as well as visual inspection of the alignment in the PyMOL molecular viewer. By using these modules, students will learn more about enzyme active sites (catalytic sites). ProMOL also allows them to build their own active site templates to further explore their proteins of unknown function.

Module Resources

Download student module here

Key Points

  • Your students will use a computer alignment algorithm that includes quantitative measures (Levenshtein distance and RMSD values) and visual inspection to measure quality of alignments.

  • These results can be compared and contrasted with sequence alignment (BLAST, Pfam) and and full backbone alignment (Dali) results in other BASIL modules.

  • This module requires that you to install PyMOL and ProMOL on student-accessible computers and requires internet access.