Protein folds and protein folding

R. Dustin Schaeffer, Valerie Daggett

Research output: Contribution to journalReview articlepeer-review

48 Scopus citations


The classification of protein folds is necessarily based on the structural elements that distinguish domains. Classification of protein domains consists of two problems: the partition of structures into domains and the classification of domains into sets of similar structures (or folds). Although similar topologies may arise by convergent evolution, the similarity of their respective folding pathways is unknown. The discovery and the characterization of the majority of protein folds will be followed by a similar enumeration of available protein folding pathways. Consequently, understanding the intricacies of structural domains is necessary to understanding their collective folding pathways. We review the current state of the art in the field of protein domain classification and discuss methods for the systematic and comprehensive study of protein folding across protein fold space via atomistic molecular dynamics simulation. Finally, we discuss our large-scale Dynameomics project, which includes simulations of representatives of all autonomous protein folds. 2010

Original languageEnglish (US)
Pages (from-to)11-19
Number of pages9
JournalProtein Engineering, Design and Selection
Issue number1-2
StatePublished - Jan 2011


  • molecular dynamics simulations
  • protein folding
  • protein folds
  • structural classification

ASJC Scopus subject areas

  • Biotechnology
  • Bioengineering
  • Biochemistry
  • Molecular Biology


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