Configurational temperature density of states simulations of proteins.
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Summary
A novel method to compute the density of states of proteins by integrating the reciprocal of temperature and it is found that the proposed method is more efficient than earlier, related schemes for simulation of protein folding.
- Type
- article
- Published
- 2003-12-01
- Cited by
- 34
- References
- 25
- Access
- Open access
- OpenAlex
- https://openalex.org/W2013828699
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:2319629
Keywords
Statistical physics, Representation (politics), Force field (fiction), Physics, Chemistry
References
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- Density of states simulations of proteins
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- Multicanonical algorithms for first order phase transitions
- Multicanonical procedure for continuum peptide models
- Hyperparallel tempering Monte Carlo simulation of polymeric systems
- Configurational temperature: Verification of Monte Carlo simulations
- Microscopic expressions for the thermodynamic temperature
- Understanding beta-hairpin formation.
- Monte Carlo simulations in generalized ensemble: Multicanonical algorithm versus simulated tempering.
- Molecular dynamics simulations of unfolding and refolding of a beta-hairpin fragment of protein G.
- Effective energy function for proteins in solution
- Comparison of three Monte Carlo conformational search strategies for a proteinlike homopolymer model: Folding thermodynamics and identification of low-energy structures
- Evaluation of a fast implicit solvent model for molecular dynamics simulations
- CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
Cited by
- Monte Carlo simulations.
- Molecular Modeling of DNA for a Mechanistic Understanding of Hybridization
- A parallel implementation of the Wang-Landau algorithm
- Novel procedure for thermal equilibration in molecular dynamics simulation
- Convergence of molecular dynamics simulations of membrane proteins
- Flux Tempered Metadynamics
- Structure and stability of a model three‐helix‐bundle protein on tailored surfaces
- Polypeptide foldings obtained with effective pair potentials.
- Confinement effects on the thermodynamics of protein folding: Monte Carlo simulations.
- Molecular simulation of the reversible mechanical unfolding of proteins.
- Optimal allocation of replicas in parallel tempering simulations.
- An entropic perspective of protein stability on surfaces.
- Parallel tempering Monte Carlo simulations of lysozyme orientation on charged surfaces.
- Improved Wang-Landau sampling through the use of smoothed potential-energy surfaces.
- Some comments on Monte Carlo and molecular dynamics methods
- A novel method reveals that solvent water favors polyproline II over β‐strand conformation in peptides and unfolded proteins: conditional hydrophobic accessible surface area (CHASA)
- Density of states-based molecular simulations.
- Effect of Surface Curvature and Chemistry on Protein Stability, Adsorption and Aggregation
- A molecular view of the role of chirality in charge-driven polypeptide complexation.
- ZIBgridfree - Adaptive Conformation Analysis with qualified Support of Transition States and Thermodynamic Weights