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Methods Mol Biol. 2017;1529:203-214.

Applications of Normal Mode Analysis Methods in Computational Protein Design.

Author information

1
Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts avenue, Cambridge, MA, 02139, USA.
2
Faculty of Medicine and Health Sciences, Department of Biochemistry, University of Sherbrooke, 3001, 12 Av., NordSherbrooke, QCJ1H 5N4, Canada.
3
Department of Pharmacology and Physiology, Faculty of Medicine, Université de Montreal, Montreal, H3C 3J7, QC, Canada. rafael.najmanovich@umontreal.ca.
4
Faculty of Medicine and Health Sciences, Department of Biochemistry, University of Sherbrooke, 3001, 12 Av., NordSherbrooke, QCJ1H 5N4, Canada. rafael.najmanovich@umontreal.ca.

Abstract

Recent advances in coarse-grained normal mode analysis methods make possible the large-scale prediction of the effect of mutations on protein stability and dynamics as well as the generation of biologically relevant conformational ensembles. Given the interplay between flexibility and enzymatic activity, the combined analysis of stability and dynamics using the Elastic Network Contact Model (ENCoM) method has ample applications in protein engineering in industrial and medical applications such as in computational antibody design. Here, we present a detailed tutorial on how to perform such calculations using ENCoM.

KEYWORDS:

Mutations; Normal mode analysis; Protein dynamics; Protein engineering; Protein stability; Vibrational entropy

PMID:
27914052
DOI:
10.1007/978-1-4939-6637-0_9
[Indexed for MEDLINE]

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