ArticleBiophysical journal2009
Secondary structure propensities in peptide folding simulations: a systematic comparison of molecular mechanics interaction schemes.
Article in Biophysical journal, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 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
30 citing papers in PubMed.
- How Well Do Molecular Dynamics Force Fields Model Peptides: A Systematic Benchmark across Diverse Folding Behaviors.The journal of physical chemistry. B · 2026Article
- A molecular dynamics study of cell-penetrating peptide transportan-10 (TP10): Binding, folding and insertion to transmembrane state in zwitterionic membrane.Biochimica et biophysica acta. Biomembranes · 2024Article
- Current Approaches in Supersecondary Structures Investigation.International journal of molecular sciences · 2021Review
- Length Dependent Folding Kinetics of Alanine-Based Helical Peptides from Optimal Dimensionality Reduction.Life (Basel, Switzerland) · 2021Article
- Structural and thermodynamic analysis of factors governing the stability and thermal folding/unfolding of SazCA.PloS one · 2021Article
- Benchmark assessment of molecular geometries and energies from small molecule force fields.F1000Research · 2020Article
- Effects of All-Atom Molecular Mechanics Force Fields on Amyloid Peptide Assembly: The Case of AβJournal of chemical theory and computation · 2019Article
- Peptide and Protein Structure Prediction with a Simplified Continuum Solvent Model.The journal of physical chemistry. B · 2018Article
- Folding Molecular Dynamics Simulation of a gp41-Derived Peptide Reconcile Divergent Structure Determinations.ACS omega · 2018Article
- Multiscale modeling of keratin, collagen, elastin and related human diseases: Perspectives from atomistic to coarse-grained molecular dynamics simulations.Extreme Mechanics Letters · 2018Article
- A theoretical study of the unfolding pathway of reduced human serum albumin.Journal of molecular modeling · 2015Article
- Using D-Amino Acids to Delineate the Mechanism of Protein Folding: Application to Trp-cage.Chemical physics · 2013Article
- Comparison of the structural characteristics of Cu(2+)-bound and unbound α-syn12 peptide obtained in simulations using different force fields.Journal of molecular modeling · 2013Article
- Stability of transmembrane amyloid β-peptide and membrane integrity tested by molecular modeling of site-specific Aβ42 mutations.PloS one · 2013Article
- Inclusion of many-body effects in the additive CHARMM protein CMAP potential results in enhanced cooperativity of α-helix and β-hairpin formation.Biophysical journal · 2012Article
- DelPhi: a comprehensive suite for DelPhi software and associated resources.BMC biophysics · 2012Article
- Force Field Benchmark of Organic Liquids: Density, Enthalpy of Vaporization, Heat Capacities, Surface Tension, Isothermal Compressibility, Volumetric Expansion Coefficient, and Dielectric Constant.Journal of chemical theory and computation · 2012Article
- Intramolecular interactions stabilizing compact conformations of the intrinsically disordered kinase-inhibitor domain of Sic1: a molecular dynamics investigation.Frontiers in physiology · 2012Article
- β-hairpin forms by rolling up from C-terminal: topological guidance of early folding dynamics.Scientific reports · 2012Article
- Molecular dynamics simulations of voltage-gated cation channels: insights on voltage-sensor domain function and modulation.Frontiers in pharmacology · 2012Article
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
No grant is acknowledged in the PubMed record.
Abstract
We present a systematic study directed toward the secondary structure propensity and sampling behavior in peptide folding simulations with eight different molecular dynamics force-field variants in explicit solvent. We report on the combinational result of force field, water model, and electrostatic interaction schemes and compare to available experimental characterization of five studied model peptides in terms of reproduced structure and dynamics. The total simulation time exceeded 18 mus and included simulations that started from both folded and extended conformations. Despite remaining sampling issues, a number of distinct trends in the folding behavior of the peptides emerged. Pronounced differences in the propensity of finding prominent secondary structure motifs in the different applied force fields suggest that problems point in particular to the balance of the relative stabilities of helical and extended conformations.
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.