Ergodicity and model quality in template‐restrained canonical and temperature/Hamiltonian replica exchange coarse‐grained molecular dynamics simulations of proteins
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Summary
It has been found that non‐ergodicity does not affect model quality if good templates are used to generate restraints, however, when poor‐quality restraints not covering the entire protein are used, the improved ergodicity of HREMD can lead to significantly improved protein models.
- Type
- article
- Published
- 2017-09-22
- Cited by
- 8
- References
- 63
- OpenAlex
- https://openalex.org/W2758104042
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:4911953
Keywords
Ergodicity, Replica, Molecular dynamics, Statistical physics, Hamiltonian (control theory)
References
- Sigma-RF: prediction of the variability of spatial restraints in template-based modeling by random forest
- Maximum entropy approach to the determination of solution conformation of flexible polypeptides by global conformational analysis and NMR spectroscopy – Application to DNS1-c-[d-A2bu2, Trp4,Leu5]- enkephalin and DNS1-c-[d-A2bu2, Trp4, d-Leu5]enkephalin
- The ten most wanted solutions in protein bioinformatics
- Protein Structure Prediction Using Rosetta
- Protein structure modeling for CASP10 by multiple layers of global optimization
- Molecular dynamics with the united-residue model of polypeptide chains. I. Lagrange equations of motion and tests of numerical stability in the microcanonical mode.
- Improvement of the treatment of loop structures in the UNRES force field by inclusion of coupling between backbone- and side-chain-local conformational states
- Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling
- Optimized explicit-solvent replica exchange molecular dynamics from scratch.
- Exploring the Parameter Space of the Coarse-Grained UNRES Force Field by Random Search: Selecting a Transferable Medium-Resolution Force Field
- High accuracy template based modeling by global optimization
- Hierarchical Grouping to Optimize an Objective Function
- A unified coarse-grained model of biological macromolecules based on mean-field multipole–multipole interactions
- Determination of side-chain-rotamer and side-chain and backbone virtual-bond-stretching potentials of mean force from AM1 energy surfaces of terminally-blocked amino-acid residues, for coarse-grained simulations of protein structure and folding. 1. The Method
- Cumulant-based expressions for the multibody terms for the correlation between local and electrostatic interactions in the united-residue force field
- Modification and optimization of the united-residue (UNRES) potential energy function for canonical simulations. I. Temperature dependence of the effective energy function and tests of the optimization method with single training proteins.
- Segment assembly, structure alignment and iterative simulation in protein structure prediction
- Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing.
- Application of Multiplexed Replica Exchange Molecular Dynamics to the UNRES Force Field: Tests with α and α+β Proteins
- Replica-exchange molecular dynamics method for protein folding
Cited by
- A general method for the derivation of the functional forms of the effective energy terms in coarse-grained energy functions of polymers. III. Determination of scale-consistent backbone-local and correlation potentials in the UNRES force field and force-field calibration and validation.
- Introduction of a bounded penalty function in contact‐assisted simulations of protein structures to omit false restraints
- Properties of monomeric Aβ42 probed by different sampling methods and force fields: Role of energy components
- Theory and Practice of Coarse-Grained Molecular Dynamics of Biologically Important Systems
- Modeling the Structure, Dynamics, and Transformations of Proteins with the UNRES Force Field.
- A coarse‐grained approach to NMR‐data‐assisted modeling of protein structures
- Pragmatic Coarse-Graining of Proteins: Models and Applications.
- Physics-Based Coarse-Grained Modeling in Bio- and Nanochemistry
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