Protein structure modeling with MODELLER

Methods Mol Biol. 2008:426:145-59. doi: 10.1007/978-1-60327-058-8_8.


Genome sequencing projects have resulted in a rapid increase in the number of known protein sequences. In contrast, only about one-hundredth of these sequences have been characterized using experimental structure determination methods. Computational protein structure modeling techniques have the potential to bridge this sequence-structure gap. This chapter presents an example that illustrates the use of MODELLER to construct a comparative model for a protein with unknown structure. Automation of similar protocols (correction of protcols) has resulted in models of useful accuracy for domains in more than half of all known protein sequences.

MeSH terms

  • Amino Acid Sequence
  • Models, Molecular*
  • Molecular Sequence Data
  • Protein Conformation*
  • Protein Folding
  • Proteins / chemistry*
  • Proteins / ultrastructure*
  • Sequence Homology, Amino Acid
  • Software*


  • Proteins