CHARMM-GUI MDFF/xMDFF Utilizer for Molecular Dynamics Flexible Fitting Simulations in Various Environments

Yifei Qi, Jumin Lee, Abhishek Singharoy, Ryan McGreevy, Klaus Schulten, Wonpil Im

Research output: Contribution to journalArticle

6 Citations (Scopus)

Abstract

X-ray crystallography and cryo-electron microscopy are two popular methods for the structure determination of biological molecules. Atomic structures are derived through the fitting and refinement of an initial model into electron density maps constructed by both experiments. Two computational approaches, MDFF and xMDFF, have been developed to facilitate this process by integrating the experimental data with molecular dynamics simulation. However, the setup of an MDFF/xMDFF simulation requires knowledge of both experimental and computational methods, which is not straightforward for nonexpert users. In addition, sometimes it is desirable to include realistic environments, such as explicit solvent and lipid bilayers during the simulation, which poses another challenge even for expert users. To alleviate these difficulties, we have developed MDFF/xMDFF Utilizer in CHARMM-GUI that helps users to set up an MDFF/xMDFF simulation. The capability of MDFF/xMDFF Utilizer is greatly enhanced by integration with other CHARMM-GUI modules, including protein structure manipulation, a diverse set of lipid types, and all-atom CHARMM and coarse-grained PACE force fields. With this integration, various simulation environments are available for MDFF Utilizer (vacuum, implicit/explicit solvent, and bilayers) and xMDFF Utilizer (vacuum and solution). In this work, three examples are shown to demonstrate the usage of MDFF/xMDFF Utilizer.

Original languageEnglish (US)
Pages (from-to)3718-3723
Number of pages6
JournalJournal of Physical Chemistry B
Volume121
Issue number15
DOIs
StatePublished - Apr 20 2017
Externally publishedYes

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graphical user interface
Molecular Dynamics Simulation
Vacuum
Graphical user interfaces
Molecular dynamics
molecular dynamics
Cryoelectron Microscopy
Lipid bilayers
X ray crystallography
X Ray Crystallography
Lipid Bilayers
Computational methods
Lipids
Electron microscopy
Carrier concentration
lipids
Physics and Chemistry Experiment in Space
simulation
Electrons
Proteins

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry
  • Surfaces, Coatings and Films
  • Materials Chemistry

Cite this

CHARMM-GUI MDFF/xMDFF Utilizer for Molecular Dynamics Flexible Fitting Simulations in Various Environments. / Qi, Yifei; Lee, Jumin; Singharoy, Abhishek; McGreevy, Ryan; Schulten, Klaus; Im, Wonpil.

In: Journal of Physical Chemistry B, Vol. 121, No. 15, 20.04.2017, p. 3718-3723.

Research output: Contribution to journalArticle

Qi, Yifei ; Lee, Jumin ; Singharoy, Abhishek ; McGreevy, Ryan ; Schulten, Klaus ; Im, Wonpil. / CHARMM-GUI MDFF/xMDFF Utilizer for Molecular Dynamics Flexible Fitting Simulations in Various Environments. In: Journal of Physical Chemistry B. 2017 ; Vol. 121, No. 15. pp. 3718-3723.
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