ArticleJournal of structural biology2011
Applications of the molecular dynamics flexible fitting method.
Article in Journal of structural biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
What it found
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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.
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Who cites it
34 citing papers in PubMed, 44 citations in OpenAlex.
- A structural biology compatible file format for atomic force microscopy.Nature communications · 2025Article
- Elucidating structural variability in p53 conformers using combinatorial refinement strategies and molecular dynamics.Cancer biology & therapy · 2024Article
- 3D variability analysis reveals a hidden conformational change controlling ammonia transport in human asparagine synthetase.Nature communications · 2024Article
- 3D Variability Analysis Reveals a Hidden Conformational Change Controlling Ammonia Transport in Human Asparagine Synthetase.bioRxiv : the preprint server for biology · 2024Article
- From simple to complex: Reconstructing all-atom structures from coarse-grained models using cg2all.Structure (London, England : 1993) · 2024Article
- RETRACTED: Delineating Conformational Variability in Small Protein Structures Using Combinatorial Refinement StrategiesMicromachines · 2023Article
- Refinement of a cryo-EM structure of hERG: Bridging structure and function.Biophysical journal · 2021Article
- Scalable molecular dynamics on CPU and GPU architectures with NAMD.The Journal of chemical physics · 2020Article
- Simulation-Based Methods for Model Building and Refinement in Cryoelectron Microscopy.Journal of chemical information and modeling · 2020Review
- Measurement of atom resolvability in cryo-EM maps with Q-scores.Nature methods · 2020Article
- Capsid expansion of bacteriophage T5 revealed by high resolution cryoelectron microscopy.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Predicting Protein Complex Structure from Surface-Induced Dissociation Mass Spectrometry Data.ACS central science · 2019Article
- Constructing atomic structural models into cryo-EM densities using molecular dynamics - Pros and cons.Journal of structural biology · 2018Article
- CryoEM structure of MxB reveals a novel oligomerization interface critical for HIV restriction.Science advances · 2017Article
- Molecular dynamics-based refinement and validation for sub-5 Å cryo-electron microscopy maps.eLife · 2016Article
- The C-Terminal Arm of the Human Papillomavirus Major Capsid Protein Is Immunogenic and Involved in Virus-Host Interaction.Structure (London, England : 1993) · 2016Article
- Macromolecular Crystallography for Synthetic Abiological Molecules: Combining xMDFF and PHENIX for Structure Determination of Cyanostar Macrocycles.Journal of the American Chemical Society · 2015Article
- Improved cryoEM-Guided Iterative Molecular Dynamics--Rosetta Protein Structure Refinement Protocol for High Precision Protein Structure Prediction.Journal of chemical theory and computation · 2015Article
- Integrative Modeling of Macromolecular Assemblies from Low to Near-Atomic Resolution.Computational and structural biotechnology journal · 2015Review
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Corrections and comments
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Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
Abstract
In recent years, cryo-electron microscopy (cryo-EM) has established itself as a key method in structural biology, permitting the structural characterization of large biomolecular complexes in various functional states. The data obtained through single-particle cryo-EM has recently seen a leap in resolution thanks to landmark advances in experimental and computational techniques, resulting in sub-nanometer resolution structures being obtained routinely. The remaining gap between these data and revealing the mechanisms of molecular function can be closed through hybrid modeling tools that incorporate known atomic structures into the cryo-EM data. One such tool, molecular dynamics flexible fitting (MDFF), uses molecular dynamics simulations to combine structures from X-ray crystallography with cryo-EM density maps to derive atomic models of large biomolecular complexes. The structures furnished by MDFF can be used subsequently in computational investigations aimed at revealing the dynamics of the complexes under study. In the present work, recent applications of MDFF are presented, including the interpretation of cryo-EM data of the ribosome at different stages of translation and the structure of a membrane-curvature-inducing photosynthetic complex.
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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.