Elfin: an algorithm for the computational design of custom three-dimensional structures from modular repeat protein building blocks

Chun Ting Yeh, T. J. Brunette, David Baker, Simon McIntosh-Smith, Fabio Parmeggiani*

*Corresponding author for this work

Research output: Contribution to journalArticle (Academic Journal)peer-review

5 Citations (Scopus)
263 Downloads (Pure)

Abstract

Computational protein design methods have enabled the design of novel protein structures, but they are often still limited to small proteins and symmetric systems. To expand the size of designable proteins while controlling the overall structure, we developed Elfin, a genetic algorithm for the design of novel proteins with custom shapes using structural building blocks derived from experimentally verified repeat proteins. By combining building blocks with compatible interfaces, it is possible to rapidly build non-symmetric large structures (> 1000 amino acids) that match three-dimensional geometric descriptions provided by the user. A run time of about 20 minutes on a laptop computer for a 3000 amino acid structure makes Elfin accessible to users with limited computational resources. Protein structures with controlled geometry will allow the systematic study of the effect of spatial arrangement of enzymes and signaling molecules, and provide new scaffolds for functional nanomaterials.
Original languageEnglish
Pages (from-to)100-107
Number of pages8
JournalJournal of Structural Biology
Volume201
Issue number2
Early online date7 Sep 2017
DOIs
Publication statusPublished - 1 Feb 2018

Structured keywords

  • Bristol BioDesign Institute
  • BrisSynBio

Keywords

  • Repeat protein
  • Protein design
  • Protein origami
  • Genetic algorithm
  • Computational protein design
  • SYNTHETIC BIOLOGY

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