ArticleWiley interdisciplinary reviews. Computational molecular science
Molecular Dynamics Simulations of Macromolecular Crystals.
Article in Wiley interdisciplinary reviews. Computational molecular science. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 46 citations in OpenAlex.
- AI-Predicted Model-Guided Rebuilding of the Experimental Structure of Mouse δ-Aminolevulinic Acid Dehydratase.International journal of molecular sciences · 2026Article
- Molecular neighbours reshape protein dynamics.Nature chemistry · 2026Article
- Aromatic ring flips reveal reshaping of protein dynamics in crystals and complexes.Nature chemistry · 2026Article
- Interactions of Cyclic Peptides Ribifolin and Gramicidin S with Montmorillonite Surface by Molecular Modeling.ACS omega · 2026Article
- Semi-automated modeling of reaction states in time-resolved serial femtosecond crystallography using molecular dynamics sampled conformations.Structural dynamics (Melville, N.Y.) · 2025Article
- Structure-Based Experimental Datasets for Benchmarking Protein Simulation Force Fields [Article v1.0].Living journal of computational molecular science · 2025Article
- Functional protein dynamics in a crystal.Nature communications · 2024Article
- Functional Protein Dynamics in a Crystal.bioRxiv : the preprint server for biology · 2024Article
- Network pharmacology and in vitro experimental verification unveil glycyrrhizin from glycyrrhiza glabra alleviates acute pancreatitis via modulation of MAPK and STAT3 signaling pathways.BMC complementary medicine and therapies · 2024Article
- LAWS: Local alignment for water sites-Tracking ordered water in simulations.Biophysical journal · 2023Article
- Emerging Time-Resolved X-Ray Diffraction Approaches for Protein Dynamics.Annual review of biophysics · 2023Review
- Torsion angles to map and visualize the conformational space of a protein.Protein science : a publication of the Protein Society · 2023Article
- Article
- Physicochemical Heuristics for Identifying High Fidelity, Near-Native Structural Models of Peptide/MHC Complexes.Frontiers in immunology · 2022Article
- Targeting Bromodomain and Extraterminal Proteins for Drug Discovery: From Current Progress to Technological Development.Journal of medicinal chemistry · 2021Review
- Hydration and its Hydrogen Bonding State on a Protein Surface in the Crystalline State as Revealed by Molecular Dynamics Simulation.Frontiers in chemistry · 2021Article
- Advances in methods for atomic resolution macromolecular structure determination.F1000Research · 2020Review
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2 authors at 1 institution in 1 country.
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Abstract
The structures of biological macromolecules would not be known to their present extent without X-ray crystallography. Most simulations of globular proteins in solution begin by surrounding the crystal structure of the monomer in a bath of water molecules, but the standard simulation employing periodic boundary conditions is already close to a crystal lattice environment. With simple protocols, the same software and molecular models can perform simulations of the crystal lattice, including all asymmetric units and solvent to fill the box. Throughout the history of molecular dynamics, studies of crystal lattices have served to investigate the quality of the underlying force fields, correlate the simulated ensembles to experimental structure factors, and extrapolate the behavior in lattices to behavior in solution. Powerful new computers are enabling molecular simulations with greater realism and statistical convergence. Meanwhile, the advent of exciting new methods in crystallography, including femtosecond free-electron lasers and image reconstruction for time-resolved crystallography on slurries of small crystals, is expanding the range of structures accessible to X-ray diffraction. We review past fusions of simulations and crystallography, then look ahead to the ways that simulations of crystal structures will enhance structural biology in the future.
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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.