ArticleJournal of computational chemistry2015
Force field-dependent solution properties of glycine oligomers.
Article in Journal of computational chemistry, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
15 citing papers in PubMed.
- Effects of Conformational Constraint on Peptide Solubility Limits.The journal of physical chemistry. B · 2022Article
- Thermodynamic Compensation in Peptides Following Liquid-Liquid Phase Separation.The journal of physical chemistry. B · 2021Article
- Physical Chemistry of the Protein Backbone: Enabling the Mechanisms of Intrinsic Protein Disorder.The journal of physical chemistry. B · 2020Review
- The lac repressor hinge helix in context: The effect of the DNA binding domain and symmetry.Biochimica et biophysica acta. General subjects · 2020Article
- Improvements to the ABSINTH Force Field for Proteins Based on Experimentally Derived Amino Acid Specific Backbone Conformational Statistics.Journal of chemical theory and computation · 2019Article
- Price of disorder in the lac repressor hinge helix.Biopolymers · 2019Article
- Thermodynamics of Conformational Transitions in a Disordered Protein Backbone Model.Biophysical journal · 2018Article
- Peptide Solubility Limits: Backbone and Side-Chain Interactions.The journal of physical chemistry. B · 2018Article
- HyRes: a coarse-grained model for multi-scale enhanced sampling of disordered protein conformations.Physical chemistry chemical physics : PCCP · 2017Article
- Intramolecular Interactions Overcome Hydration to Drive the Collapse Transition of GlyThe journal of physical chemistry. B · 2017Article
- Crowding in Cellular Environments at an Atomistic Level from Computer Simulations.The journal of physical chemistry. B · 2017Article
- Nonpolar Solvation Free Energy from Proximal Distribution Functions.The journal of physical chemistry. B · 2017Article
- Effect of methyl groups on conformational properties of small ionized comb-like polyelectrolytes at the atomic level.Journal of molecular modeling · 2017Article
- Solvation Thermodynamics of Oligoglycine with Respect to Chain Length and Flexibility.Biophysical journal · 2016Article
- Importance of Hydrophilic Hydration and Intramolecular Interactions in the Thermodynamics of Helix-Coil Transition and Helix-Helix Assembly in a Deca-Alanine Peptide.The journal of physical chemistry. B · 2016Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
Abstract
Molecular simulations can be used to study disordered polypeptide systems and to generate hypotheses on the underlying structural and thermodynamic mechanisms that govern their function. As the number of disordered protein systems investigated with simulations increase, it is important to understand how particular force fields affect the structural properties of disordered polypeptides in solution. To this end, we performed a comparative structural analysis of Gly(3) and Gly(10) in aqueous solution from all atom, microsecond molecular dynamics (MD) simulations using the CHARMM 27 (C27), CHARMM 36 (C36), and Amber ff12SB force fields. For each force field, Gly(3) and Gly(10) were simulated for at least 300 ns and 1 μs, respectively. Simulating oligoglycines of two different lengths allows us to evaluate how force field effects depend on polypeptide length. Using a variety of structural metrics (e.g., end-to-end distance, radius of gyration, dihedral angle distributions), we characterize the distribution of oligoglycine conformers for each force field and show that each sample conformation space differently, yielding considerably different structural tendencies of the same oligoglycine model in solution. Notably, we find that C36 samples more extended oligoglycine structures than both C27 and ff12SB.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.