dTERMen—design with TERM energies

About dTERMen

dTERMen is a method for performing computational protein design that is based on TERMs. A TERM (short for tertiary motif) is a fragment of protein structure, consistent of one or more disjoint structural segments, that is reused across unrelated proteins. This reuse, which we described in several studies [1-2], allows one to directly mine the Protein Data Bank (PDB) for sequence-structure relationships. Specifically, repeated TERM instances allow us to identify sequence features necessary for stabilizing the corresponding structural motif. And because any desired target structure T can be broken down into its constituent TERMs, we can combine the sequence-structure relationships learned from the individual TERMs to build a model for what sequences would most likely stabilize T. dTERMen is based on this general concept.

Getting dTERMen

dTERMen, which makes heavy use of our structure search engine MASTER [3], is freely available to non-commercial entities. To obtain the software, please contact the Dartmouth College Technology Transfer Office at Technology.transfer@dartmouth.edu and note that you are looking to get dTERMen.

Citing dTERMen

If you use dTERMen in your work, please cite:

"A general-purpose protein design framework based on mining sequence-structure relationships in known protein structures", J. Zhou, A. E. Panaitiu, G. Grigoryan, PNAS, 2019 [DOI].


  • [1] "Tertiary Alphabet for the Observable Protein Structural Universe", C. O. Mackenzie, J. Zhou, G. Grigoryan, Proceedings of the National Academy of Sciences, 113(47): E7438-E7447, 2016.

  • [2] "Tertiary Structural Propensities Reveal Fundamental Sequence/Structure Relationships", F. Zheng, J. Zhang, G. Grigoryan, Structure, 23(5): 961-971, 2015.

  • [3] "Rapid Search for Tertiary Fragments Reveals Protein Sequence-Structure Relationships", J. Zhou, G. Grigoryan, Protein Science, 24(4): 508-524, 2015.