ArticlePloS one2014
Evaluation of unrestrained replica-exchange simulations using dynamic walkers in temperature space for protein structure refinement.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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8 citing papers in PubMed, 15 citations in OpenAlex.
- Semi-automated modeling of reaction states in time-resolved serial femtosecond crystallography using molecular dynamics sampled conformations.Structural dynamics (Melville, N.Y.) · 2025Article
- Improved Sampling Strategies for Protein Model Refinement Based on Molecular Dynamics Simulation.Journal of chemical theory and computation · 2021Article
- Sequence Tolerance of a Single-Domain Antibody with a High Thermal Stability: Comparison of Computational and Experimental Fitness Profiles.ACS omega · 2019Article
- Methods for the Refinement of Protein Structure 3D Models.International journal of molecular sciences · 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
- On the Helix Propensity in Generalized Born Solvent Descriptions of Modeling the Dark Proteome.Frontiers in molecular biosciences · 2017Article
- Protein structure refinement via molecular-dynamics simulations: What works and what does not?Proteins · 2016Article
- Computational protein structure refinement: Almost there, yet still so far to go.Wiley interdisciplinary reviews. Computational molecular scienceArticle
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Authors and funding
2 authors at 2 institutions in 1 country.
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Abstract
A central problem of computational structural biology is the refinement of modeled protein structures taken from either comparative modeling or knowledge-based methods. Simulations are commonly used to achieve higher resolution of the structures at the all-atom level, yet methodologies that consistently yield accurate results remain elusive. In this work, we provide an assessment of an adaptive temperature-based replica exchange simulation method where the temperature clients dynamically walk in temperature space to enrich their population and exchanges near steep energetic barriers. This approach is compared to earlier work of applying the conventional method of static temperature clients to refine a dataset of conformational decoys. Our results show that, while an adaptive method has many theoretical advantages over a static distribution of client temperatures, only limited improvement was gained from this strategy in excursions of the downhill refinement regime leading to an increase in the fraction of native contacts. To illustrate the sampling differences between the two simulation methods, energy landscapes are presented along with their temperature client profiles.
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