ArticleJournal of chemical theory and computation2015
Improved cryoEM-Guided Iterative Molecular Dynamics--Rosetta Protein Structure Refinement Protocol for High Precision Protein Structure Prediction.
Article in Journal of chemical theory and computation, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- Fast activity prediction of chemically modified siRNAs via structure-based energy calculations and inference-augmented tabular deep learning.Molecular therapy. Nucleic acids · 2026Article
- NMR-Chemical-Shift-Driven Protocol Reveals the Cofactor-Bound, Complete Structure of Dynamic Intermediates of the Catalytic Cycle of Oncogenic KRAS G12C Protein and the Significance of the MgInternational journal of molecular sciences · 2023Article
- Efficient Flexible Fitting Refinement with Automatic Error Fixing for De Novo Structure Modeling from Cryo-EM Density Maps.Journal of chemical information and modeling · 2021Article
- Structural insights into photosystem II assembly.Nature plants · 2021Article
- Hybrid methods for combined experimental and computational determination of protein structure.The Journal of chemical physics · 2020Review
- Using NMR Chemical Shifts and Cryo-EM Density Restraints in Iterative Rosetta-MD Protein Structure Refinement.Journal of chemical information and modeling · 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
- Simulation-Based Methods for Model Building and Refinement in Cryoelectron Microscopy.Journal of chemical information and modeling · 2020Review
- Improving the Efficiency of Ligand-Binding Protein Design with Molecular Dynamics Simulations.Journal of chemical theory and computation · 2019Article
- Predicting Protein Complex Structure from Surface-Induced Dissociation Mass Spectrometry Data.ACS central science · 2019Article
- Measuring Intrinsic Disorder and Tracking Conformational Transitions Using Rosetta ResidueDisorder.The journal of physical chemistry. B · 2019Article
- Utility of Covalent Labeling Mass Spectrometry Data in Protein Structure Prediction with Rosetta.Journal of chemical theory and computation · 2019Article
- Expanded Coverage of the 26S Proteasome Conformational Landscape Reveals Mechanisms of Peptidase Gating.Cell reports · 2018Article
- Rosetta Protein Structure Prediction from Hydroxyl Radical Protein Footprinting Mass Spectrometry Data.Analytical chemistry · 2018Article
- CryoEM-based hybrid modeling approaches for structure determination.Current opinion in microbiology · 2018Review
- Accurately Predicting Disordered Regions of Proteins Using Rosetta ResidueDisorder Application.The journal of physical chemistry. B · 2018Article
- Combined approaches from physics, statistics, and computer science forF1000Research · 2018Review
- Iterative Molecular Dynamics-Rosetta Membrane Protein Structure Refinement Guided by Cryo-EM Densities.Journal of chemical theory and computation · 2017Article
- CryoEM structure of MxB reveals a novel oligomerization interface critical for HIV restriction.Science advances · 2017Article
- CryoEM Structure Refinement by Integrating NMR Chemical Shifts with Molecular Dynamics Simulations.The journal of physical chemistry. B · 2017Article
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2 authors.
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Abstract
Many excellent methods exist that incorporate cryo-electron microscopy (cryoEM) data to constrain computational protein structure prediction and refinement. Previously, it was shown that iteration of two such orthogonal sampling and scoring methods – Rosetta and molecular dynamics (MD) simulations – facilitated exploration of conformational space in principle. Here, we go beyond a proof-of-concept study and address significant remaining limitations of the iterative MD–Rosetta protein structure refinement protocol. Specifically, all parts of the iterative refinement protocol are now guided by medium-resolution cryoEM density maps, and previous knowledge about the native structure of the protein is no longer necessary. Models are identified solely based on score or simulation time. All four benchmark proteins showed substantial improvement through three rounds of the iterative refinement protocol. The best-scoring final models of two proteins had sub-Ångstrom RMSD to the native structure over residues in secondary structure elements. Molecular dynamics was most efficient in refining secondary structure elements and was thus highly complementary to the Rosetta refinement which is most powerful in refining side chains and loop regions.
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