Studies of an Off-Lattice Model for Protein Folding: Sequence Dependence and Improved Sampling at Finite Temperature
arXiv:chem-ph/9505003 · doi:10.1063/1.469931
Abstract
We study the thermodynamic behavior of a simple off-lattice model for protein folding. The model is two-dimensional and has two different ``amino acids''. Using numerical simulations of all chains containing eight or ten monomers, we examine the sequence dependence at a fixed temperature. It is shown that only a few of the chains exist in unique folded state at this temperature, and the energy level spectra of chains with different types of behavior are compared. Furthermore, we use this model as a testbed for two improved Monte Carlo algorithms. Both algorithms are based on letting some parameter of the model become a dynamical variable; one of the algorithms uses a fluctuating temperature and the other a fluctuating monomer sequence. We find that by these algorithms one gains large factors in efficiency in comparison with conventional methods.
17 pages, 9 Postscript figures. Combined with chem-ph/9505004
References in corpus (8)
- Simulated Tempering: A New Monte Carlo Scheme
- Multicanonical Ensemble: A New Approach to Simulate First-order Phase Transitions
- Critical Exponents, Hyperscaling and Universal Amplitude Ratios for Two- and Three-Dimensional Self-Avoiding Walks
- Comparative Study of Multicanonical and Simulated Annealing Algorithms in the Protein Folding Problem
- Simulated-tempering approach to spin-glass simulations
- Hybrid Monte Carlo simulation of polymer chains
- Phase transition and dynamical-parameter method in U(1) gauge theory
- Cluster dynamics for first-order phase transitions in the Potts model
Cited by in corpus (32)
- Multidimensional replica-exchange method for free-energy calculations
- Folding Trp-cage to NMR resolution native structure using a coarse-grained model
- Oligomerization of amyloid Abeta peptides using hydrogen bonds and hydrophobicity forces
- Three-helix-bundle Protein in a Ramachandran Model
- Local Interactions and Protein Folding: A 3D Off-Lattice Approach
- Monte Carlo Update for Chain Molecules: Biased Gaussian Steps in Torsional Space
- Folding thermodynamics of peptides
- Structure optimization in an off-lattice protein model
- Replica-Exchange Simulated Tempering Method for Simulations of Frustrated Systems
- Protein folding using contact maps
- Thermodynamics of alpha- and beta-structure formation in proteins
- Identification of Amino Acid Sequences with Good Folding Properties in an Off-Lattice Model
- Monte Carlo Study of the Phase Structure of Compact Polymer Chains
- Mean-Field HP Model, Designability and Alpha-Helices in Protein Structures
- Monte Carlo Procedure for Protein Design
- Hydrogen Bonds in Polymer Folding
- Irreversible simulated tempering
- Two-state folding over a weak free-energy barrier
- Thermally activated processes in polymer dynamics
- Exploring the energy landscape of model proteins: a metric criterion for the determination of dynamical connectivity
- Generalized-ensemble simulations of spin systems and protein systems
- An Efficient Simulation Protocol for Determining the Density of States: Combination of Replica-Exchange Wang-Landau Method and Multicanonical Replica-Exchange Method
- Simulated tempering with irreversible Gibbs sampling techniques
- Folding thermodynamics of three beta-sheet peptides: A model study
- Design of Sequences with Good Folding Properties in Coarse-Grained Protein Models
- A Minimal Off-Lattice Model for Alpha-helical Proteins
- Enhanced Sampling Algorithms
- Sequence-based study of two related proteins with different folding behaviors
- Two-dimensional simulated tempering for the isobaric-isothermal ensemble with fast on-the-fly weight determination
- Folding of a Small Helical Protein Using Hydrogen Bonds and Hydrophobicity Forces
- Folding and Design in Coarse-Grained Protein Models
- Hydrogen Bonds, Hydrophobicity Forces and the Character of the Collapse Transition