Comparative Protein Structure Modeling Using MODELLER

Curr Protoc Bioinformatics. 2016 Jun 20:54:5.6.1-5.6.37. doi: 10.1002/cpbi.3.


Comparative protein structure modeling predicts the three-dimensional structure of a given protein sequence (target) based primarily on its alignment to one or more proteins of known structure (templates). The prediction process consists of fold assignment, target-template alignment, model building, and model evaluation. This unit describes how to calculate comparative models using the program MODELLER and how to use the ModBase database of such models, and discusses all four steps of comparative modeling, frequently observed errors, and some applications. Modeling lactate dehydrogenase from Trichomonas vaginalis (TvLDH) is described as an example. The download and installation of the MODELLER software is also described. © 2016 by John Wiley & Sons, Inc.

Keywords: MODELLER; ModBase; comparative modeling; protein fold; protein structure; structure prediction.

MeSH terms

  • Amino Acid Sequence
  • Chemistry Techniques, Analytical / methods*
  • L-Lactate Dehydrogenase / chemistry
  • Models, Molecular*
  • Protein Conformation
  • Proteins / chemistry*
  • Sequence Alignment
  • Software
  • Trichomonas vaginalis / enzymology


  • Proteins
  • L-Lactate Dehydrogenase