Challenges in computational studies of enzyme structure, function and dynamics

Alexandra T.P. Carvalho, Alexandre Barrozo, Dvir Doron, Alexandra Vardi Kilshtain, Dan Thomas Major, Shina Caroline Lynn Kamerlin

Research output: Contribution to journalArticlepeer-review

51 Scopus citations

Abstract

In this review we give an overview of the field of Computational enzymology. We start by describing the birth of the field, with emphasis on the work of the 2013 chemistry Nobel Laureates. We then present key features of the state-of-the-art in the field, showing what theory, accompanied by experiments, has taught us so far about enzymes. We also briefly describe computational methods, such as quantum mechanics-molecular mechanics approaches, reaction coordinate treatment, and free energy simulation approaches. We finalize by discussing open questions and challenges.

Original languageEnglish
Pages (from-to)62-79
Number of pages18
JournalJournal of Molecular Graphics and Modelling
Volume54
DOIs
StatePublished - Nov 2014

Bibliographical note

Publisher Copyright:
© 2014, Elsevier Inc. All rights reserved.

Keywords

  • Computational enzymology
  • Conformational sampling
  • Free energy simulations
  • QM/MM
  • Reaction coordinates

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