ArticleJournal of structural biology2013
Targeted conformational search with map-restrained self-guided Langevin dynamics: application to flexible fitting into electron microscopic density maps.
Article in Journal of structural biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
- Self-Guided Molecular Simulation to Enhance Concerted Motion.International journal of molecular sciences · 2025Article
- Structure of a 28.5 kDa duplex-embedded G-quadruplex system resolved to 7.4 Å resolution with cryo-EM.Nucleic acids research · 2023Article
- Colicin E1 opens its hinge to plug TolC.eLife · 2022Article
- A hybrid approach to study large conformational transitions of biomolecules from single particle XFEL diffraction data.Frontiers in molecular biosciences · 2022Article
- Reconstruction of Coupled Intra- and Interdomain Protein Motion from Nuclear and Electron Magnetic Resonance.Journal of the American Chemical Society · 2021Article
- Refinement of RNA Structures Using Amber Force Fields.Crystals · 2021Article
- HnRNP A1/A2 Proteins Assemble onto 7SK snRNA via Context Dependent Interactions.Journal of molecular biology · 2021Article
- Molecular Dynamics to Predict Cryo-EM: Capturing Transitions and Short-Lived Conformational States of Biomolecules.Frontiers in molecular biosciences · 2021Article
- Structural basis of Focal Adhesion Kinase activation on lipid membranes.The EMBO journal · 2020Article
- Reformulation of the self-guided molecular simulation method.The Journal of chemical physics · 2020Article
- The structure and oxidation of the eye lens chaperone αA-crystallin.Nature structural & molecular biology · 2019Article
- Article
- DFMD: Fast and Effective DelPhiForce Steered Molecular Dynamics Approach to Model Ligand Approach Toward a Receptor: Application to Spermine Synthase Enzyme.Frontiers in molecular biosciences · 2019Article
- Searching for 3D structural models from a library of biological shapes using a few 2D experimental images.BMC bioinformatics · 2018Article
- Structure of theProceedings of the National Academy of Sciences of the United States of America · 2018Article
- Enhanced Sampling of Interdomain Motion Using Map-Restrained Langevin Dynamics and NMR: Application to Pin1.Journal of molecular biology · 2018Article
- Atomic Resolution Cryo-EM Structure of β-Galactosidase.Structure (London, England : 1993) · 2018Article
- Tools for the cryo-EM gold rush: going from the cryo-EM map to the atomistic model.Bioscience reports · 2017Review
- HnRNP A1 Alters the Structure of a Conserved Enterovirus IRES Domain to Stimulate Viral Translation.Journal of molecular biology · 2017Article
- Flexible Fitting of Atomic Models into Cryo-EM Density Maps Guided by Helix Correspondences.Biophysical journal · 2017Article
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5 authors.
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Abstract
We present a map-restrained self-guided Langevin dynamics (MapSGLD) simulation method for efficient targeted conformational search. The targeted conformational search represents simulations under restraints defined by experimental observations and/or by user specified structural requirements. Through map-restraints, this method provides an efficient way to maintain substructures and to set structure targets during conformational searching. With an enhanced conformational searching ability of self-guided Langevin dynamics, this approach is suitable for simulating large-scale conformational changes, such as the formation of macromolecular assemblies and transitions between different conformational states. Using several examples, we illustrate the application of this method in flexible fitting of atomic structures into density maps derived from cryo-electron microscopy.
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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.