Are current molecular dynamics force fields too helical?
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Summary
Simulation of Ala(5) in water finds that most current force fields do overpopulate the alpha-region, with quantitative results depending on the choice of Karplus relation and on the peptide termini, while experiments on short peptides open the way toward the systematic improvement of current simulation models.
- Type
- article
- Published
- 2008-07-01
- Cited by
- 424
- References
- 24
- Access
- Open access
- OpenAlex
- https://openalex.org/W1985070997
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:41587889
Keywords
Current (fluid), Dynamics (music), Molecular dynamics, Force field (fiction), Physics
References
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- Molecular dynamics simulations of biomolecules
- How Large is an α-Helix? Studies of the Radii of Gyration of Helical Peptides by Small-angle X-ray Scattering and Molecular Dynamics
- Calculation of NMR-relaxation parameters for flexible molecules from molecular dynamics simulations
- Helix‐coil transition of alanine peptides in water: Force field dependence on the folded and unfolded structures
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- Constrained Unfolding of a Helical Peptide: Implicit versus Explicit Solvents
- Characterizing the Conformational Landscape of Flavivirus Fusion Peptides via Simulation and Experiment
- Ca2+ binding induced sequential allosteric activation of sortase A: An example for ion-triggered conformational selection
- Computational Approaches To Anti-Toxin Therapies And Biomarker Identification
- Computational modeling of phosphotransfer complexes in two-component signaling.
- IDENTIFICATION OF PHARMACOLOGICAL TARGETS COMBINING DOCKING AND MOLECULAR DYNAMICS SIMULATIONS
- Using Energy Landscape Theory to Uncover the Organization of Conformational Space of Proteins in Their Native States.
- A Review of Physics-Based Coarse-Grained Potentials for the Simulations of Protein Structure and Dynamics
- Conformational dynamics of two natively unfolded fragment peptides: Comparison of the AMBER and CHARMM force fields
- Predicting conformational ensembles of the intrinsically disordered protein α-Synuclein via molecular simulation
- Action of the anticancer drug cisplatin investigated by molecular simulation
- Insights into the Binding of Intrinsically Disordered Proteins from Molecular Dynamics Simulation
- Epitopes, aggregation and membrane binding: investigating the protein structure-function relationship
- Nascent β-Hairpin Formation of a Natively Unfolded Peptide Reveals the Role of Hydrophobic Contacts
- Secondary Structure of Rat and Human Amylin across Force Fields
- Development of accurate and efficient models for biological molecules
- Motional timescale predictions by molecular dynamics simulations: Case study using proline and hydroxyproline sidechain dynamics
- Alzheimer's amyloid-β and the disordered structural ensemble characterized using molecular dynamics and NMR spectroscopy
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