Computational techniques to study protein dynamics and conformations

Anil Mhashal, Agusti Emperador, Laura Orellana

Research output: Chapter in Book/Report/Conference proceedingChapterpeer-review


Protein dynamics and conformational transitions are essential for most biological functions. They are the necessary link to connect atomic-level structural details with cellular processes ranging from enzymatic catalysis to signaling, solute transport, or synaptic transmission. In this chapter, we review standard atomistic and coarse-grained techniques of increasing complexity to simulate protein motions and conformational transitions. We present the key theoretical foundations and compare how different standard methods explore the conformational landscape in the case of a protein with known intermediates for a simple conformational change. The goal is to provide nonspecialist readers with a broad overview of available approaches that can be used to obtain a basic assessment of protein flexibility.

Original languageEnglish
Title of host publicationAdvances in Protein Molecular and Structural Biology Methods
Number of pages14
ISBN (Electronic)9780323902649
ISBN (Print)9780323902656
StatePublished - 1 Jan 2022
Externally publishedYes

Bibliographical note

Publisher Copyright:
© 2022 Elsevier Inc. All rights reserved.


  • Brownian dynamics
  • Coarse-graining
  • Conformational transitions
  • Discrete dynamics
  • Molecular dynamics
  • Normal mode analysis
  • Protein dynamics


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