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The Framework of Computational Protein Design

Part of the Methods in Molecular Biology book series (MIMB,volume 1529)

Abstract

Computational protein design (CPD) has established itself as a leading field in basic and applied science with a strong coupling between the two. Proteins are computationally designed from the level of amino acids to the level of a functional protein complex. Design targets range from increased thermo- (or other) stability to specific requested reactions such as protein–protein binding, enzymatic reactions, or nanotechnology applications. The design scheme may encompass small regions of the proteins or the entire protein. In either case, the design may aim at the side-chains or at the full backbone conformation. Herein, the main framework for the process is outlined highlighting key elements in the CPD iterative cycle. These include the very definition of CPD, the diverse goals of CPD, components of the CPD protocol, methods for searching sequence and structure space, scoring functions, and augmenting the CPD with other optimization tools. Taken together, this chapter aims to introduce the framework of CPD.

Key words

  • Computational protein design
  • Protein structure prediction
  • Structural bioinformatics
  • Computational biophysics
  • Synthetic biology
  • Negative design

“Most people make the mistake of thinking design is what it looks like. People think it’s this veneer—that the designers are handed this box and told, ‘Make it look good!’ That’s not what we think design is. It’s not just what it looks like and feels like. Design is how it works.” Steve Jobs, Apple’s C.E.O in an interview to the New-York Times. Nov. 30th 2003, The Guts of a New Machine

http://www.nytimes.com/2003/11/30/magazine/the-guts-of-a-new-machine.html

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Samish, I. (2017). The Framework of Computational Protein Design. In: Samish, I. (eds) Computational Protein Design. Methods in Molecular Biology, vol 1529. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6637-0_1

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