ArticleMethods (San Diego, Calif.)2009
Molecular dynamics flexible fitting: a practical guide to combine cryo-electron microscopy and X-ray crystallography.
Article in Methods (San Diego, Calif.), 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 244 papers.
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244 citing papers in PubMed.
- Article
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- Lenacapavir prevents production of infectious HIV-1 by abrogating immature virus assembly.bioRxiv : the preprint server for biology · 2026Article
- Comparing Multislice Projections of MD Simulations with CryoEM Exposes Structural Prediction Errors.bioRxiv : the preprint server for biology · 2026Article
- Probing the role of membrane in neutralizing activity of antibodies against influenza virus.Structure (London, England : 1993) · 2026Article
- Transient protein structure guides surface diffusion pathways for electron transport in membrane supercomplexes.Nature communications · 2026Article
- CryoAtom improves model building for cryo-EM.Nature structural & molecular biology · 2026Article
- Cryo-electron microscopy ensemble optimization using individual particles and physical constraints.bioRxiv : the preprint server for biology · 2025Article
- Distinct Target Site of Lenacapavir in Immature HIV-1 and Concurrent Binding with the Maturation Inhibitor Bevirimat.Journal of the American Chemical Society · 2025Article
- 4D structural biology-quantitative dynamics in the eukaryotic RNA exosome complex.Nature communications · 2025Article
- A comprehensive survey and benchmark of deep learning-based methods for atomic model building from cryo-electron microscopy density maps.Briefings in bioinformatics · 2025Article
- Ensemble refinement of mismodeled cryo-EM RNA structures using all-atom simulations.Nature communications · 2025Article
- Structural maturation of the matrix lattice is not required for HIV-1 particle infectivity.Science advances · 2025Article
- Transport of phenoxyacetic acid herbicides by PIN-FORMED auxin transporters.Nature plants · 2025Article
- Structural architecture of TolQ-TolR inner membrane protein complex from opportunistic pathogenScience advances · 2025Article
- MELD in Action: Harnessing Data to Accelerate Molecular Dynamics.Journal of chemical information and modeling · 2025Review
184 more citing papers are in PubMed but not listed here.
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5 authors.
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Abstract
Hybrid computational methods for combining structural data from different sources and resolutions are becoming an essential part of structural biology, especially as the field moves toward the study of large macromolecular assemblies. We have developed the molecular dynamics flexible fitting (MDFF) method for combining high-resolution atomic structures with cryo-electron microscopy (cryo-EM) maps, that results in atomic models representing the conformational state captured by cryo-EM. The method has been applied successfully to the ribosome, a ribonucleoprotein complex responsible for protein synthesis. MDFF involves a molecular dynamics simulation in which a guiding potential, based on the cryo-EM map, is added to the standard force field. Forces proportional to the gradient of the density map guide an atomic structure, available from X-ray crystallography, into high-density regions of a cryo-EM map. In this paper we describe the necessary steps to set up, run, and analyze MDFF simulations and the software packages that implement the corresponding functionalities.
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