Molecular dynamics with the united-residue model of polypeptide chains. II. Langevin and Berendsen-bath dynamics and tests on model alpha-helical systems.
about
My 65 years in protein chemistryLessons from application of the UNRES force field to predictions of structures of CASP10 targetsImprovement of the treatment of loop structures in the UNRES force field by inclusion of coupling between backbone- and side-chain-local conformational states.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.From helix-coil transitions to protein folding.Peierls-Nabarro barrier and protein loop propagation.An improved functional form for the temperature scaling factors of the components of the mesoscopic UNRES force field for simulations of protein structure and dynamics.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. IIInvestigation of protein folding by coarse-grained molecular dynamics with the UNRES force fieldImplementation of molecular dynamics and its extensions with the coarse-grained UNRES force field on massively parallel systems; towards millisecond-scale simulations of protein structure, dynamics, and thermodynamics.Performance of protein-structure predictions with the physics-based UNRES force field in CASP11.Coarse-grained force field: general folding theory.Kinks, loops, and protein folding, with protein A as an example.Molecular dynamics of protein A and a WW domain with a united-residue model including hydrodynamic interactionIn situ data analytics and indexing of protein trajectories.Revised Backbone-Virtual-Bond-Angle Potentials to Treat the l- and d-Amino Acid Residues in the Coarse-Grained United Residue (UNRES) Force FieldEvidence, from simulations, of a single state with residual native structure at the thermal denaturation midpoint of a small globular proteinA unified coarse-grained model of biological macromolecules based on mean-field multipole-multipole interactions.Mechanism of fiber assembly: treatment of Aβ peptide aggregation with a coarse-grained united-residue force field.PDZ binding to the BAR domain of PICK1 is elucidated by coarse-grained molecular dynamics.Physics-based potentials for the coupling between backbone- and side-chain-local conformational states in the UNited RESidue (UNRES) force field for protein simulations.Molecular modeling of the binding modes of the iron-sulfur protein to the Jac1 co-chaperone from Saccharomyces cerevisiae by all-atom and coarse-grained approachesHidden protein folding pathways in free-energy landscapes uncovered by network analysis.Simulation of the opening and closing of Hsp70 chaperones by coarse-grained molecular dynamicsCoexistence of phases in a protein heterodimerDetermination of effective potentials for the stretching of C(α) ⋯ C(α) virtual bonds in polypeptide chains for coarse-grained simulations of proteins from ab initio energy surfaces of N-methylacetamide and N-acetylpyrrolidineEffects of mutation, truncation, and temperature on the folding kinetics of a WW domain.Relation between free energy landscapes of proteins and dynamics.Replica Exchange and Multicanonical Algorithms with the coarse-grained UNRES force field.Molecular dynamics with the united-residue model of polypeptide chains. I. Lagrange equations of motion and tests of numerical stability in the microcanonical mode.Implementations of Nosé-Hoover and Nosé-Poincaré thermostats in mesoscopic dynamic simulations with the united-residue model of a polypeptide chainMolecular dynamics with the United-residue force field: ab initio folding simulations of multichain proteinsLocal vs global motions in protein foldingPrincipal component analysis for protein folding dynamicsExploring the parameter space of the coarse-grained UNRES force field by random search: selecting a transferable medium-resolution force field.Implementation of a Serial Replica Exchange Method in a Physics-Based United-Residue (UNRES) Force Field.Folding and self-assembly of a small heterotetramerExtension of UNRES force field to treat polypeptide chains with D-amino-acid residues.Application of Multiplexed Replica Exchange Molecular Dynamics to the UNRES Force Field: Tests with alpha and alpha+beta Proteins.Prediction of protein structure with the coarse-grained UNRES force field assisted by small X-ray scattering data and knowledge-based information.
P2860
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P2860
Molecular dynamics with the united-residue model of polypeptide chains. II. Langevin and Berendsen-bath dynamics and tests on model alpha-helical systems.
description
2005 nî lūn-bûn
@nan
2005年の論文
@ja
2005年論文
@yue
2005年論文
@zh-hant
2005年論文
@zh-hk
2005年論文
@zh-mo
2005年論文
@zh-tw
2005年论文
@wuu
2005年论文
@zh
2005年论文
@zh-cn
name
Molecular dynamics with the un ...... n model alpha-helical systems.
@en
type
label
Molecular dynamics with the un ...... n model alpha-helical systems.
@en
prefLabel
Molecular dynamics with the un ...... n model alpha-helical systems.
@en
P2860
P356
P1476
Molecular dynamics with the un ...... n model alpha-helical systems.
@en
P2093
Anna Jagielska
Mey Khalili
P2860
P304
13798-13810
P356
10.1021/JP058007W
P407
P577
2005-07-01T00:00:00Z