ArticleJournal of chemical theory and computation2013
Iterative Molecular Dynamics-Rosetta Protein Structure Refinement Protocol to Improve Model Quality.
Article in Journal of chemical theory and computation, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Three-dimensional architecture of ESCRT-III flat spirals on the membrane.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Computational biology and artificial intelligence in mRNA vaccine design for cancer immunotherapy.Frontiers in cellular and infection microbiology · 2024Review
- 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
- Integrating comparative modeling and accelerated simulations reveals conformational and energetic basis of actomyosin force generation.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Annealing synchronizes the 70Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Computational prediction of the effect of amino acid changes on the binding affinity between SARS-CoV-2 spike RBD and human ACE2.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Structural plasticity of mumps virus nucleocapsids with cryo-EM structures.Communications biology · 2021Article
- Structure and assembly of double-headed Sendai virus nucleocapsids.Communications biology · 2021Article
- Identification of Novel Cyclin A2 Binding Site and Nanomolar Inhibitors of Cyclin A2-CDK2 Complex.Current computer-aided drug design · 2021Article
- Hybrid methods for combined experimental and computational determination of protein structure.The Journal of chemical physics · 2020Review
- Harnessing Conformational Plasticity to Generate Designer Enzymes.Journal of the American Chemical Society · 2020Review
- Enhancing aChemical science · 2020Article
- Using NMR Chemical Shifts and Cryo-EM Density Restraints in Iterative Rosetta-MD Protein Structure Refinement.Journal of chemical information and modeling · 2020Article
- Practical Considerations for Atomistic Structure Modeling with Cryo-EM Maps.Journal of chemical information and modeling · 2020Article
- 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
- Experimental accuracy in protein structure refinement via molecular dynamics simulations.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Accurately Predicting Disordered Regions of Proteins Using Rosetta ResidueDisorder Application.The journal of physical chemistry. B · 2018Article
- Iterative Molecular Dynamics-Rosetta Membrane Protein Structure Refinement Guided by Cryo-EM Densities.Journal of chemical theory and computation · 2017Article
- Protein Folding and Structure Prediction from the Ground Up II: AAWSEM for α/β Proteins.The journal of physical chemistry. B · 2017Article
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Authors and funding
3 authors.
Funding
Abstract
Rosetta is one of the prime tools for high resolution protein structure refinement. While its scoring function can distinguish native-like from non-native-like conformations in many cases, the method is limited by conformational sampling for larger proteins, that is, leaving a local energy minimum in which the search algorithm may get stuck. Here, we test the hypothesis that iteration of Rosetta with an orthogonal sampling and scoring strategy might facilitate exploration of conformational space. Specifically, we run short molecular dynamics (MD) simulations on models created by
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