ArticleThe journal of physical chemistry. B2017
CHARMM-GUI MDFF/xMDFF Utilizer for Molecular Dynamics Flexible Fitting Simulations in Various Environments.
Article in The journal of physical chemistry. B, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 30 citations in OpenAlex.
- CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed.The journal of physical chemistry. B · 2024Review
- MDFF_NM: Improved Molecular Dynamics Flexible Fitting into Cryo-EM Density Maps with a Multireplica Normal Mode-Based Search.Journal of chemical information and modeling · 2024Article
- Pharmacological inhibition of Kir4.1 evokes rapid-onset antidepressant responses.Nature chemical biology · 2024Article
- Molecular dynamics simulations of lipid-protein interactions in SLC4 proteins.Biophysical journal · 2024Article
- One bead per residue can describe all-atom protein structures.Structure (London, England : 1993) · 2024Article
- Automated simulation-based membrane protein refinement into cryo-EM data.Biophysical journal · 2023Article
- pyCHARMM: Embedding CHARMM Functionality in a Python Framework.Journal of chemical theory and computation · 2023Article
- CryoEM structures of anion exchanger 1 capture multiple states of inward- and outward-facing conformations.Communications biology · 2022Article
- Bridging the N-terminal and middle domains in FliG of the flagellar rotor.Current research in structural biology · 2022Article
- Computational Resources for Bioscience Education.Applied biochemistry and biotechnology · 2021Article
- Cryo-EM structure of the sodium-driven chloride/bicarbonate exchanger NDCBE.Nature communications · 2021Article
- Refinement of a cryo-EM structure of hERG: Bridging structure and function.Biophysical journal · 2021Article
- Flexible Fitting of Small Molecules into Electron Microscopy Maps Using Molecular Dynamics Simulations with Neural Network Potentials.Journal of chemical information and modeling · 2020Article
- CryoEM maps are full of potential.Current opinion in structural biology · 2019Review
- Constructing atomic structural models into cryo-EM densities using molecular dynamics - Pros and cons.Journal of structural biology · 2018Article
- Article
- Asymmetric Cryo-EM Structure of Anthrax Toxin Protective Antigen Pore with Lethal Factor N-Terminal Domain.Toxins · 2017Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.