Protein Structure Modeling With MODELLER

Methods Mol Biol. 2017;1654:39-54. doi: 10.1007/978-1-4939-7231-9_4.

Abstract

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 at atomic resolution using experimental structure determination methods. Computational protein structure modeling techniques have the potential to bridge this sequence-structure gap. In the following chapter, we present an example that illustrates the use of MODELLER to construct a comparative model for a protein with unknown structure. Automation of a similar protocol has resulted in models of useful accuracy for domains in more than half of all known protein sequences.

Keywords: Comparative modeling; Fold assignment; Model assessment; Multiple templates; Sequence-structure alignment.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Amino Acid Sequence
  • Models, Molecular
  • Protein Conformation
  • Proteins / chemistry*
  • Software

Substances

  • Proteins