ArticleProceedings of the National Academy of Sciences of the United States of America2018
Experimental accuracy in protein structure refinement via molecular dynamics simulations.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
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44 citing papers in PubMed, 88 citations in OpenAlex.
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- Protein structure and folding pathway prediction based on remote homologs recognition using PAthreader.Communications biology · 2023Article
- Implementation of Telescoping Boxes in Adaptive Steered Molecular Dynamics.Journal of chemical theory and computation · 2022Article
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- gmxapi: A GROMACS-native Python interface for molecular dynamics with ensemble and plugin support.PLoS computational biology · 2022Article
- A tale of solving two computational challenges in protein science: neoantigen prediction and protein structure prediction.Briefings in bioinformatics · 2022Review
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- Molecular dynamics: a powerful tool for studying the medicinal chemistry of ion channel modulators.RSC medicinal chemistry · 2021Review
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Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Refinement is the last step in protein structure prediction pipelines to convert approximate homology models to experimental accuracy. Protocols based on molecular dynamics (MD) simulations have shown promise, but current methods are limited to moderate levels of consistent refinement. To explore the energy landscape between homology models and native structures and analyze the challenges of MD-based refinement, eight test cases were studied via extensive simulations followed by Markov state modeling. In all cases, native states were found very close to the experimental structures and at the lowest free energies, but refinement was hindered by a rough energy landscape. Transitions from the homology model to the native states require the crossing of significant kinetic barriers on at least microsecond time scales. A significant energetic driving force toward the native state was lacking until its immediate vicinity, and there was significant sampling of off-pathway states competing for productive refinement. The role of recent force field improvements is discussed and transition paths are analyzed in detail to inform which key transitions have to be overcome to achieve successful refinement.
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