ReviewAnnual review of biophysics2016
Computational Methodologies for Real-Space Structural Refinement of Large Macromolecular Complexes.
Review in Annual review of biophysics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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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
41 citing papers in PubMed.
- From Atoms to Cells: AI-Based Structure Prediction Fueling Molecular Dynamics Simulations in Computational Structural Biology.Advances in experimental medicine and biology · 2026Review
- Generative AI for computational chemistry: A roadmap to predicting emergent phenomena.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- In-cell structure and variability of pyrenoid Rubisco.Nature communications · 2025Article
- In-cell Structure and Variability of Pyrenoid Rubisco.bioRxiv : the preprint server for biology · 2025Article
- A structural biology compatible file format for atomic force microscopy.Nature communications · 2025Article
- AMBERff at Scale: Multimillion-Atom Simulations with AMBER Force Fields in NAMD.Journal of chemical information and modeling · 2024Article
- Fostering discoveries in the era of exascale computing: How the next generation of supercomputers empowers computational and experimental biophysics alike.Biophysical journal · 2023Review
- Engineering excitonically coupled dimers in an artificial protein for light harvesting via computational modeling.Protein science : a publication of the Protein Society · 2023Article
- Cryo-electron Microscopy of Adeno-associated Virus.Chemical reviews · 2022Review
- Allosteric control of Ubp6 and the proteasome via a bidirectional switch.Nature communications · 2022Article
- Protein structure prediction in the era of AI: Challenges and limitations when applying toFrontiers in bioinformatics · 2022Article
- Lessons Learned from Responsive Molecular Dynamics Studies of the COVID-19 Virus.Proceedings of UrgentHPC 2021 : the Third International Workshop on HPC for Urgent Decision Making · 2021Article
- CryoFold: determining protein structures and data-guided ensembles from cryo-EM density maps.Matter · 2021Article
- Multi-Scale Flexible Fitting of Proteins to Cryo-EM Density Maps at Medium Resolution.Frontiers in molecular biosciences · 2021Article
- Large-Scale Molecular Dynamics Simulations of Cellular Compartments.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Cryo-EM and MD infer water-mediated proton transport and autoinhibition mechanisms of VScience advances · 2020Article
- Coronavirus through Delaware's Computational Microscope.Delaware journal of public health · 2020Article
- Flexible Fitting of Small Molecules into Electron Microscopy Maps Using Molecular Dynamics Simulations with Neural Network Potentials.Journal of chemical information and modeling · 2020Article
- Article
- High-Performance Analysis of Biomolecular Containers to Measure Small-Molecule Transport, Transbilayer Lipid Diffusion, and Protein Cavities.Journal of chemical information and modeling · 2019Article
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
The rise of the computer as a powerful tool for model building and refinement has revolutionized the field of structure determination for large biomolecular systems. Despite the wide availability of robust experimental methods capable of resolving structural details across a range of spatiotemporal resolutions, computational hybrid methods have the unique ability to integrate the diverse data from multimodal techniques such as X-ray crystallography and electron microscopy into consistent, fully atomistic structures. Here, commonly employed strategies for computational real-space structural refinement are reviewed, and their specific applications are illustrated for several large macromolecular complexes: ribosome, virus capsids, chemosensory array, and photosynthetic chromatophore. The increasingly important role of computational methods in large-scale structural refinement, along with current and future challenges, is discussed.
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Registered trials
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