ArticlePloS one2015
Comparing molecular dynamics force fields in the essential subspace.
Article in PloS one, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed.
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- Opportunities and challenges in modelling ligand adsorption on semiconductor nanocrystals.Communications chemistry · 2025Review
- Anion-Facilitated Hydrogen-Deuterium Exchange as a Tool to Probe Weak Anion-Protein Interactions Responsible for Hofmeister Effects.The journal of physical chemistry. B · 2025Article
- APACE: AlphaFold2 and advanced computing as a service for accelerated discovery in biophysics.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Exploiting the Fc base of IgG antibodies to create functional nanoparticle conjugates.Scientific reports · 2024Article
- Assessing Weak Anion Binding to Small Peptides.The journal of physical chemistry. B · 2024Article
- TRAP1 S-nitrosylation as a model of population-shift mechanism to study the effects of nitric oxide on redox-sensitive oncoproteins.Cell death & disease · 2023Article
- Mechanistic basis of GPCR activation explored by ensemble refinement of crystallographic structures.Protein science : a publication of the Protein Society · 2022Article
- Characterization of the non-covalent interaction between the PF-07321332 inhibitor and the SARS-CoV-2 main protease.Journal of molecular graphics & modelling · 2022Article
- Force Field Effects in Simulations of Flexible Peptides with Varying Polyproline II Propensity.Journal of chemical theory and computation · 2021Article
- The conformational and mutational landscape of the ubiquitin-like marker for autophagosome formation in cancer.Autophagy · 2021Article
- Molecular dynamics: a powerful tool for studying the medicinal chemistry of ion channel modulators.RSC medicinal chemistry · 2021Review
- Epistatic interactions promote persistence of NS3-Q80K in HCV infection by compensating for protein folding instability.The Journal of biological chemistry · 2021Article
- Biomolecular Simulations with the Three-Dimensional Reference Interaction Site Model with the Kovalenko-Hirata Closure Molecular Solvation Theory.International journal of molecular sciences · 2021Review
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- Cationic Dendrimers for siRNA Delivery: Computational Approaches for Characterization.Methods in molecular biology (Clifton, N.J.) · 2021Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The continued development and utility of molecular dynamics simulations requires improvements in both the physical models used (force fields) and in our ability to sample the Boltzmann distribution of these models. Recent developments in both areas have made available multi-microsecond simulations of two proteins, ubiquitin and Protein G, using a number of different force fields. Although these force fields mostly share a common mathematical form, they differ in their parameters and in the philosophy by which these were derived, and previous analyses showed varying levels of agreement with experimental NMR data. To complement the comparison to experiments, we have performed a structural analysis of and comparison between these simulations, thereby providing insight into the relationship between force-field parameterization, the resulting ensemble of conformations and the agreement with experiments. In particular, our results show that, at a coarse level, many of the motional properties are preserved across several, though not all, force fields. At a finer level of detail, however, there are distinct differences in both the structure and dynamics of the two proteins, which can, together with comparison with experimental data, help to select force fields for simulations of proteins. A noteworthy observation is that force fields that have been reparameterized and improved to provide a more accurate energetic description of the balance between helical and coil structures are difficult to distinguish from their "unbalanced" counterparts in these simulations. This observation implies that simulations of stable, folded proteins, even those reaching 10 microseconds in length, may provide relatively little information that can be used to modify torsion parameters to achieve an accurate balance between different secondary structural elements.
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