ArticleJournal of chemical information and modeling2020
Using NMR Chemical Shifts and Cryo-EM Density Restraints in Iterative Rosetta-MD Protein Structure Refinement.
Article in Journal of chemical information and modeling, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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15 citing papers in PubMed.
- Improving Protein Structure Determination by Integrating Ensemble-Driven Molecular Dynamics with Chemical Shift-Based Restraints.Journal of chemical information and modeling · 2026Article
- CS-DTA: a language model-driven framework for robust drug-target affinity prediction under strict cold-start scenarios.Frontiers in chemistry · 2026Article
- The State-of-the-Art Overview to Application of Deep Learning in Accurate Protein Design and Structure Prediction.Topics in current chemistry (Cham) · 2024Review
- Predicting ion mobility collision cross sections using projection approximation with ROSIE-PARCS webserver.Briefings in bioinformatics · 2023Article
- 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
- Protein shape sampled by ion mobility mass spectrometry consistently improves protein structure prediction.Nature communications · 2022Article
- CryoFold: determining protein structures and data-guided ensembles from cryo-EM density maps.Matter · 2021Article
- Utilization of Hydrophobic Microenvironment Sensitivity in Diethylpyrocarbonate Labeling for Protein Structure Prediction.Analytical chemistry · 2021Article
- State-dependent sequential allostery exhibited by chaperonin TRiC/CCT revealed by network analysis of Cryo-EM maps.Progress in biophysics and molecular biology · 2021Article
- Database Independent Automated Structure Elucidation of Organic Molecules Based on IR,Journal of chemical information and modeling · 2021Article
- Using Open Data to Rapidly Benchmark Biomolecular Simulations: Phospholipid Conformational Dynamics.Journal of chemical information and modeling · 2021Article
- Accurate protein structure prediction with hydroxyl radical protein footprinting data.Nature communications · 2021Article
- Hybrid methods for combined experimental and computational determination of protein structure.The Journal of chemical physics · 2020Review
- Practical Considerations for Atomistic Structure Modeling with Cryo-EM Maps.Journal of chemical information and modeling · 2020Article
- Faces of Contemporary CryoEM Information and Modeling.Journal of chemical information and modeling · 2020Article
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2 authors.
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Abstract
Cryo-EM has become one of the prime methods for protein structure elucidation, frequently yielding density maps with near-atomic or medium resolution. If protein structures cannot be deduced unambiguously from the density maps, computational structure refinement tools are needed to generate protein structural models. We have previously developed an iterative Rosetta-MDFF protocol that used cryo-EM densities to refine protein structures. Here we show that, in addition to cryo-EM densities, incorporation of other experimental restraints into the Rosetta-MDFF protocol further improved refined structures. We used NMR chemical shift (CS) data integrated with cryo-EM densities in our hybrid protocol in both the Rosetta step and the molecular dynamics (MD) simulations step. In 15 out of 18 cases for all MD rounds, the refinement results obtained when density maps and NMR chemical shift data were used in combination outperformed those of density map-only refinement. Notably, the improvement in refinement was highest when medium and low-resolution density maps were used. With our hybrid method, the RMSDs of final models obtained were always better than the RMSDs obtained by our previous protocol with just density refinement for both medium (6.9 Å) and low (9 Å) resolution maps. For all the six test proteins with medium resolution density maps (6.9 Å), the final refined structure RMSDs were lower for the hybrid method than for the cryo-EM only refinement. The final refined RMSDs were less than 1.5 Å when our hybrid protocol was used with 4 Å density maps. For four out of the six proteins the final RMSDs were even less than 1 Å. This study demonstrates that by using a combination of cryo-EM and NMR restraints, it is possible to refine structures to atomic resolution, outperforming single restraint refinement. This hybrid protocol will be a valuable tool when only low-resolution cryo-EM density data and NMR chemical shift data are available to refine structures.
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