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

Yeh, C, Brunette, T, Baker, D, McIntosh-Smith, S and Parmeggiani, F ORCID: https://orcid.org/0000-0001-8548-1090 2018. Elfin: An algorithm for the computational design of custom three-dimensional structures from modular repeat protein building blocks. Journal of Structural Biology X 201 (2) , pp. 100-107. 10.1016/j.jsb.2017.09.001

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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 min 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.

Item Type:	Article
Date Type:	Publication
Status:	Published
Schools:	Pharmacy
Publisher:	Elsevier {BV}
ISSN:	2590-1524
Last Modified:	16 Oct 2024 15:45
URI:	https://orca.cardiff.ac.uk/id/eprint/172227

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