Application of Multiplexed Replica Exchange Molecular Dynamics to the UNRES Force Field: Tests with alpha and alpha+beta Proteins.
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.SSThread: Template-free protein structure prediction by threading pairs of contacting secondary structures followed by assembly of overlapping pairs.WeFold: a coopetition for protein structure predictionThe LA loop as an important regulatory element of the HtrA (DegP) protease from Escherichia coli: structural and functional studies.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 fieldComputational analysis of the CB1 carboxyl-terminus in the receptor-G protein complexImplementation 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.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.Physics-based potentials for the coupling between backbone- and side-chain-local conformational states in the UNited RESidue (UNRES) force field for protein simulations.Folding helical proteins in explicit solvent using dihedral-biased tempering.Simulation of the opening and closing of Hsp70 chaperones by coarse-grained molecular dynamicsCoexistence of phases in a protein heterodimerReplica exchanging self-guided Langevin dynamics for efficient and accurate conformational samplingOptimization of a Nucleic Acids united-RESidue 2-Point model (NARES-2P) with a maximum-likelihood approachEffects of mutation, truncation, and temperature on the folding kinetics of a WW domain.Folding and self-assembly of a small protein complexFolding and self-assembly of a small heterotetramerAssessment of hard target modeling in CASP12 reveals an emerging role of alignment-based contact prediction methods.Prediction of protein structure with the coarse-grained UNRES force field assisted by small X-ray scattering data and knowledge-based information.Ergodicity and model quality in template-restrained canonical and temperature/Hamiltonian replica exchange coarse-grained molecular dynamics simulations of proteins.Simple Physics-Based Analytical Formulas for the Potentials of Mean Force of the Interaction of Amino Acid Side Chains in Water. VII. Charged-Hydrophobic/Polar and Polar-Hydrophobic/Polar Side Chains.Role of the sulfur to α-carbon thioether bridges in thurincin H.Extension of coarse-grained UNRES force field to treat carbon nanotubes.UNRES server for physics-based coarse-grained simulations and prediction of protein structure, dynamics and thermodynamics.The canonical equilibrium of constrained molecular models
P2860
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P2860
Application of Multiplexed Replica Exchange Molecular Dynamics to the UNRES Force Field: Tests with alpha and alpha+beta Proteins.
description
2009 nî lūn-bûn
@nan
2009年の論文
@ja
2009年論文
@yue
2009年論文
@zh-hant
2009年論文
@zh-hk
2009年論文
@zh-mo
2009年論文
@zh-tw
2009年论文
@wuu
2009年论文
@zh
2009年论文
@zh-cn
name
Application of Multiplexed Rep ...... alpha and alpha+beta Proteins.
@en
Application of Multiplexed Rep ...... alpha and alpha+beta Proteins.
@nl
type
label
Application of Multiplexed Rep ...... alpha and alpha+beta Proteins.
@en
Application of Multiplexed Rep ...... alpha and alpha+beta Proteins.
@nl
prefLabel
Application of Multiplexed Rep ...... alpha and alpha+beta Proteins.
@en
Application of Multiplexed Rep ...... alpha and alpha+beta Proteins.
@nl
P2860
P356
P1476
Application of Multiplexed Rep ...... alpha and alpha+beta Proteins.
@en
P2093
Cezary Czaplewski
Sebastian Kalinowski
P2860
P304
P356
10.1021/CT800397Z
P577
2009-03-01T00:00:00Z