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

Ryan McGreevy; Ivan Teo; Abhishek Singharoy; Klaus Schulten

doi:10.1016/j.ymeth.2016.01.009

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

Ryan McGreevy, Ivan Teo, Abhishek Singharoy, Klaus Schulten

Research output: Contribution to journal › Article › peer-review

68 Scopus citations

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 language	English (US)
Pages (from-to)	50-60
Number of pages	11
Journal	Methods
Volume	100
DOIs	https://doi.org/10.1016/j.ymeth.2016.01.009
State	Published - May 1 2016
Externally published	Yes

Keywords

Cryo-electron microscopy
Molecular dynamics

ASJC Scopus subject areas

Molecular Biology
General Biochemistry, Genetics and Molecular Biology

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10.1016/j.ymeth.2016.01.009

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title = "Advances in the molecular dynamics flexible fitting method for cryo-EM modeling",

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.",

keywords = "Cryo-electron microscopy, Molecular dynamics",

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note = "Funding Information: This work has been supported by grants NIH 9P41GM104601 , NIH 5R01GM098243-02 , and NIH U54GM087519 from the National Institutes of Health . The authors also acknowledge the Beckman Postdoctoral Fellowship program supporting A. Singharoy. Publisher Copyright: {\textcopyright} 2016 Elsevier Inc..",

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doi = "10.1016/j.ymeth.2016.01.009",

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AU - Teo, Ivan

AU - Singharoy, Abhishek

AU - Schulten, Klaus

N1 - Funding Information: This work has been supported by grants NIH 9P41GM104601 , NIH 5R01GM098243-02 , and NIH U54GM087519 from the National Institutes of Health . The authors also acknowledge the Beckman Postdoctoral Fellowship program supporting A. Singharoy. Publisher Copyright: © 2016 Elsevier Inc..

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

Abstract

Keywords

ASJC Scopus subject areas

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