Optimizing physical energy functions for protein folding.
about
Folding energy landscape and network dynamics of small globular proteinsNovel knowledge-based mean force potential at the profile levelModification 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.Learning To Fold Proteins Using Energy Landscape Theory.Protein structure prediction using basin-hopping.Artefacts and biases affecting the evaluation of scoring functions on decoy sets for protein structure prediction.Protein structure prediction: do hydrogen bonding and water-mediated interactions suffice?Distance dependency and minimum amino acid alphabets for decoy scoring potentials.Paddling mechanism for the substrate translocation by AAA+ motor revealed by multiscale molecular simulations.High-resolution protein complexes from integrating genomic information with molecular simulation.Building native protein conformation from highly approximate backbone torsion angles.Ab initio simulations of protein-folding pathways by molecular dynamics with the united-residue model of polypeptide chainsPredictive energy landscapes for folding α-helical transmembrane proteins.Charge density distributions derived from smoothed electrostatic potential functions: design of protein reduced point charge models.High-resolution protein folding with a transferable potential.Shaping up the protein folding funnel by local interaction: lesson from a structure prediction study.How Co-translational Folding of Multi-domain Protein Is Affected by Elongation Schedule: Molecular Simulations.Specificity quantification of biomolecular recognition and its implication for drug discovery.Topography of funneled landscapes determines the thermodynamics and kinetics of protein foldingReduced C(beta) statistical potentials can outperform all-atom potentials in decoy identification.In silico chaperonin-like cycle helps folding of proteins for structure prediction.Use of decoys to optimize an all-atom force field including hydration.Molecular dynamics with the united-residue model of polypeptide chains. I. Lagrange equations of motion and tests of numerical stability in the microcanonical mode.Funneling and frustration in the energy landscapes of some designed and simplified proteins.The multiscale coarse-graining method. II. Numerical implementation for coarse-grained molecular models.Recent advances in transferable coarse-grained modeling of proteins.Molecular mechanics.Efficient Parameter Estimation of Generalizable Coarse-Grained Protein Force Fields Using Contrastive Divergence: A Maximum Likelihood Approach.Generic coarse-grained model for protein folding and aggregation.Characterizing protein energy landscape by self-learning multiscale simulations: application to a designed β-hairpin.Simulating protein folding initiation sites using an alpha-carbon-only knowledge-based force field.Mapping all-atom models onto one-bead Coarse Grained Models: general properties and applications to a minimal polypeptide model.Separation of time scale and coupling in the motion governed by the coarse-grained and fine degrees of freedom in a polypeptide backbone.A local landscape mapping method for protein structure prediction in the HP modelCoarse-grained protein molecular dynamics simulations
P2860
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P2860
Optimizing physical energy functions for protein folding.
description
2004 nî lūn-bûn
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2004年の論文
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2004年学术文章
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2004年学术文章
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2004年学术文章
@zh-cn
2004年学术文章
@zh-hans
2004年学术文章
@zh-my
2004年学术文章
@zh-sg
2004年學術文章
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2004年學術文章
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name
Optimizing physical energy functions for protein folding.
@en
Optimizing physical energy functions for protein folding.
@nl
type
label
Optimizing physical energy functions for protein folding.
@en
Optimizing physical energy functions for protein folding.
@nl
prefLabel
Optimizing physical energy functions for protein folding.
@en
Optimizing physical energy functions for protein folding.
@nl
P356
P1433
P1476
Optimizing physical energy functions for protein folding.
@en
P2093
Shoji Takada
Yoshimi Fujitsuka
P304
P356
10.1002/PROT.10429
P407
P577
2004-01-01T00:00:00Z