ArticleActa crystallographica. Section D, Biological crystallography2014
xMDFF: molecular dynamics flexible fitting of low-resolution X-ray structures.
Article in Acta crystallographica. Section D, Biological crystallography, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
29 citing papers in PubMed.
- Article
- GOLEM: Automated and Robust Cryo-EM-Guided Ligand Docking with Explicit Water Molecules.Journal of chemical information and modeling · 2024Article
- Automated simulation-based membrane protein refinement into cryo-EM data.Biophysical journal · 2023Article
- Determining structures of individual RNA conformers using atomic force microscopy images and deep neural networks.Research square · 2023Article
- Visualizing RNA conformational and architectural heterogeneity in solution.Nature communications · 2023Article
- Article
- Assembly and Analysis of Cell-Scale Membrane Envelopes.Journal of chemical information and modeling · 2022Article
- Article
- Revealing the structures of megadalton-scale DNA complexes with nucleotide resolution.Nature communications · 2020Article
- Scalable molecular dynamics on CPU and GPU architectures with NAMD.The Journal of chemical physics · 2020Article
- Article
- The Crystal Structure of Dph2 in Complex with Elongation Factor 2 Reveals the Structural Basis for the First Step of Diphthamide Biosynthesis.Biochemistry · 2019Article
- Multiscale Simulations of Biological Membranes: The Challenge To Understand Biological Phenomena in a Living Substance.Chemical reviews · 2019Article
- Constructing atomic structural models into cryo-EM densities using molecular dynamics - Pros and cons.Journal of structural biology · 2018Article
- De novo main-chain modeling with MAINMAST in 2015/2016 EM Model Challenge.Journal of structural biology · 2018Article
- Structure of theProceedings of the National Academy of Sciences of the United States of America · 2018Article
- Assigning crystallographic electron densities with free energy calculations-The case of the fluoride channel Fluc.PloS one · 2018Article
- CHARMM-GUI 10 years for biomolecular modeling and simulation.Journal of computational chemistry · 2017Review
- CHARMM-GUI MDFF/xMDFF Utilizer for Molecular Dynamics Flexible Fitting Simulations in Various Environments.The journal of physical chemistry. B · 2017Article
- Variability of Protein Structure Models from Electron Microscopy.Structure (London, England : 1993) · 2017Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors.
Funding
Abstract
X-ray crystallography remains the most dominant method for solving atomic structures. However, for relatively large systems, the availability of only medium-to-low-resolution diffraction data often limits the determination of all-atom details. A new molecular dynamics flexible fitting (MDFF)-based approach, xMDFF, for determining structures from such low-resolution crystallographic data is reported. xMDFF employs a real-space refinement scheme that flexibly fits atomic models into an iteratively updating electron-density map. It addresses significant large-scale deformations of the initial model to fit the low-resolution density, as tested with synthetic low-resolution maps of D-ribose-binding protein. xMDFF has been successfully applied to re-refine six low-resolution protein structures of varying sizes that had already been submitted to the Protein Data Bank. Finally, via systematic refinement of a series of data from 3.6 to 7 Å resolution, xMDFF refinements together with electrophysiology experiments were used to validate the first all-atom structure of the voltage-sensing protein Ci-VSP.
Indexed as
Identifiers
What OpenQuestion holds
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.