Comparison of a QM/MM force field and molecular mechanics force fields in simulations of alanine and glycine "dipeptides" (Ace-Ala-Nme and Ace-Gly-Nme) in water in relation to the problem of modeling the unfolded peptide backbone in solution.
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The Ramachandran plots of glycine and pre-prolineLocal order in the unfolded state: conformational biases and nearest neighbor interactionsComparison of multiple Amber force fields and development of improved protein backbone parametersProtein design: Past, present, and futureFormation of partially ordered oligomers of amyloidogenic hexapeptide (NFGAIL) in aqueous solution observed in molecular dynamics simulations.Close agreement between the orientation dependence of hydrogen bonds observed in protein structures and quantum mechanical calculationsNew insights into the interdependence between amino acid stereochemistry and protein structureProtein folding by zipping and assemblyUsing quantum mechanics to improve estimates of amino acid side chain rotamer energiesConformational Preferences in Small Peptide Models: The Relevance of cis/trans-Conformations.Experimental conformational energy maps of proteins and peptides.Intrinsic backbone preferences are fully present in blocked amino acidsStrike a balance: optimization of backbone torsion parameters of AMBER polarizable force field for simulations of proteins and peptides.Origin of the neighboring residue effect on peptide backbone conformation.Deciphering protein dynamics from NMR data using explicit structure sampling and selectionA novel method reveals that solvent water favors polyproline II over beta-strand conformation in peptides and unfolded proteins: conditional hydrophobic accessible surface area (CHASA).Role of backbone solvation and electrostatics in generating preferred peptide backbone conformations: distributions of phi.Prediction of protein structure by simulating coarse-grained folding pathways: a preliminary report.Kinetics of contact formation and end-to-end distance distributions of swollen disordered peptidesEquilibrium sampling for biomolecules under mechanical tensionPotential energy functions for atomic-level simulations of water and organic and biomolecular systemsThe role of the unfolded state in hairpin stability.Polyproline II propensities from GGXGG peptides reveal an anticorrelation with beta-sheet scalesAb initio-based exciton model of amide I vibrations in peptides: definition, conformational dependence, and transferability.Populations of the three major backbone conformations in 19 amino acid dipeptides.The intrinsic conformational features of amino acids from a protein coil library and their applications in force field development.The amino acid dipeptide: small but still influential after 50 yearsA coupled two-dimensional main chain torsional potential for protein dynamics: generation and implementation.Secondary structure provides a template for the folding of nearby polypeptides.A consistent force field parameter set for zwitterionic amino acid residues.Long dynamics simulations of proteins using atomistic force fields and a continuum representation of solvent effects: calculation of structural and dynamic properties.Effect of pH on the Aggregation of α-syn12 Dimer in Explicit Water by Replica-Exchange Molecular Dynamics Simulation.Quantitative characterization of intrinsic disorder in polyglutamine: insights from analysis based on polymer theories.Hybrid quantum mechanical/molecular mechanical molecular dynamics simulations of HIV-1 integrase/inhibitor complexes.Conformational sampling of peptides in cellular environments.Reduced C(beta) statistical potentials can outperform all-atom potentials in decoy identification.Force field influences in beta-hairpin folding simulationsGeometry and Excitation Energy Fluctuations of NMA in Aqueous Solution with CHARMM, AMBER, OPLS, and GROMOS Force Fields: Implications for Protein Ultraviolet Spectra SimulationRevisiting the Ramachandran plot: hard-sphere repulsion, electrostatics, and H-bonding in the alpha-helix.Boltzmann-type distribution of side-chain conformation in proteins
P2860
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P2860
Comparison of a QM/MM force field and molecular mechanics force fields in simulations of alanine and glycine "dipeptides" (Ace-Ala-Nme and Ace-Gly-Nme) in water in relation to the problem of modeling the unfolded peptide backbone in solution.
description
2003 nî lūn-bûn
@nan
2003年の論文
@ja
2003年学术文章
@wuu
2003年学术文章
@zh-cn
2003年学术文章
@zh-hans
2003年学术文章
@zh-my
2003年学术文章
@zh-sg
2003年學術文章
@yue
2003年學術文章
@zh
2003年學術文章
@zh-hant
name
Comparison of a QM/MM force fi ...... peptide backbone in solution.
@en
Comparison of a QM/MM force fi ...... anine and glycine "dipeptides"
@nl
type
label
Comparison of a QM/MM force fi ...... peptide backbone in solution.
@en
Comparison of a QM/MM force fi ...... anine and glycine "dipeptides"
@nl
prefLabel
Comparison of a QM/MM force fi ...... peptide backbone in solution.
@en
Comparison of a QM/MM force fi ...... anine and glycine "dipeptides"
@nl
P2093
P356
P1433
P1476
Comparison of a QM/MM force fi ...... peptide backbone in solution.
@en
P2093
Jan Hermans
Marcus Elstner
P2860
P304
P356
10.1002/PROT.10279
P407
P577
2003-02-01T00:00:00Z