ArticleProteins2018
What makes it difficult to refine protein models further via molecular dynamics simulations?
Article in Proteins, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- One bead per residue can describe all-atom protein structures.Structure (London, England : 1993) · 2024Article
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- Can molecular dynamics simulations improve the structural accuracy and virtual screening performance of GPCR models?PLoS computational biology · 2021Article
- Improved Sampling Strategies for Protein Model Refinement Based on Molecular Dynamics Simulation.Journal of chemical theory and computation · 2021Article
- High throughput virtual screening reveals SARS-CoV-2 multi-target binding natural compounds to lead instant therapy for COVID-19 treatment.International journal of biological macromolecules · 2020Article
- The endoplasmic reticulum acetyltransferases ATase1/NAT8B and ATase2/NAT8 are differentially regulated to adjust engagement of the secretory pathway.Journal of neurochemistry · 2020Article
- Structural and Evolutionary Analysis Indicate That the SARS-CoV-2 Mpro Is a Challenging Target for Small-Molecule Inhibitor Design.International journal of molecular sciences · 2020Article
- Simple Selection Procedure to Distinguish between Static and Flexible Loops.International journal of molecular sciences · 2020Article
- Performance of virtual screening against GPCR homology models: Impact of template selection and treatment of binding site plasticity.PLoS computational biology · 2020Article
- Computational reconstruction of atomistic protein structures from coarse-grained models.Computational and structural biotechnology journal · 2020Review
- Driven to near-experimental accuracy by refinement via molecular dynamics simulations.Proteins · 2019Article
- Methods for the Refinement of Protein Structure 3D Models.International journal of molecular sciences · 2019Review
- Forging tools for refining predicted protein structures.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Open-Boundary Molecular Mechanics/Coarse-Grained Framework for Simulations of Low-Resolution G-Protein-Coupled Receptor-Ligand Complexes.Journal of chemical theory and computation · 2019Article
- Applications of Molecular Dynamics Simulation in Structure Prediction of Peptides and Proteins.Computational and structural biotechnology journal · 2019Review
- Experimental accuracy in protein structure refinement via molecular dynamics simulations.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Template-Guided Protein Structure Prediction and Refinement Using Optimized Folding Landscape Force Fields.Journal of chemical theory and computation · 2018Article
- Article
- Blind prediction of noncanonical RNA structure at atomic accuracy.Science advances · 2018Article
- Assessment of the model refinement category in CASP12.Proteins · 2018Article
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Authors and funding
2 authors.
Funding
Abstract
Protein structure refinement remains a challenging yet important problem as it has the potential to bring already accurate template-based models to near-native resolution. Refinement based on molecular dynamics simulations has been a highly promising approach and the performance of MD-based refinement in the Feig group during CASP12 is described here. During CASP12, sampling was extended well into the microsecond scale, an improved force field was applied, and new protocol variations were tested. Progress over previous rounds of CASP was found to be limited which is analyzed in terms of the quality of the initial models and dependency on the amount of sampling and refinement protocol variations. As current MD-based refinement protocols appear to be reaching a plateau, detailed analysis is presented to provide new insight into the major challenges towards more extensive structure refinement, focusing in particular on sampling with and without restraints.
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