Advances in the molecular dynamics flexible fitting method for cryo-EM modeling

Ryan McGreevy, Ivan Teo, Abhishek Singharoy, Klaus Schulten

Research output: Contribution to journalArticle

24 Citations (Scopus)

Abstract

Molecular Dynamics Flexible Fitting (MDFF) is an established technique for fitting all-atom structures of molecules into corresponding cryo-electron microscopy (cryo-EM) densities. The practical application of MDFF is simple but requires a user to be aware of and take measures against a variety of possible challenges presented by each individual case. Some of these challenges arise from the complexity of a molecular structure or the limited quality of available structural models and densities to be interpreted, while others stem from the intricacies of MDFF itself. The current article serves as an overview of the strategies that have been developed since MDFF's inception to overcome common challenges and successfully perform MDFF simulations.

Original languageEnglish (US)
Pages (from-to)50-60
Number of pages11
JournalMethods
Volume100
DOIs
StatePublished - May 1 2016
Externally publishedYes

Fingerprint

Cryoelectron Microscopy
Molecular Dynamics Simulation
Electron microscopy
Molecular dynamics
Structural Models
Molecular Structure
Molecular structure
Atoms
Molecules

Keywords

  • Cryo-electron microscopy
  • Molecular dynamics

ASJC Scopus subject areas

  • Molecular Biology
  • Biochemistry, Genetics and Molecular Biology(all)

Cite this

Advances in the molecular dynamics flexible fitting method for cryo-EM modeling. / McGreevy, Ryan; Teo, Ivan; Singharoy, Abhishek; Schulten, Klaus.

In: Methods, Vol. 100, 01.05.2016, p. 50-60.

Research output: Contribution to journalArticle

McGreevy, Ryan ; Teo, Ivan ; Singharoy, Abhishek ; Schulten, Klaus. / Advances in the molecular dynamics flexible fitting method for cryo-EM modeling. In: Methods. 2016 ; Vol. 100. pp. 50-60.
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