Secondary structure bias in generalized Born solvent models: comparison of conformational ensembles and free energy of solvent polarization from explicit and implicit solvation
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Protein-Ligand Electrostatic Binding Free Energies from Explicit and Implicit SolvationComputing the relative stabilities and the per-residue components in protein conformational changes.Insights on the structure and stability of Licanantase: a trimeric acid-stable coiled-coil lipoprotein from Acidithiobacillus thiooxidans.Molecular dynamics guided study of salt bridge length dependence in both fluorinated and non-fluorinated parallel dimeric coiled-coils.Folding simulations for proteins with diverse topologies are accessible in days with a physics-based force field and implicit solventCorrect folding of an α-helix and a β-hairpin using a polarized 2D torsional potential.Parameterization of an effective potential for protein-ligand binding from host-guest affinity data.Predicting peptide structures in native proteins from physical simulations of fragmentsA Partial Nudged Elastic Band Implementation for Use with Large or Explicitly Solvated SystemsThe AGBNP2 Implicit Solvation Model.Three-dimensional molecular theory of solvation coupled with molecular dynamics in Amber.Free energy of binding of coiled-coil complexes with different electrostatic environments: the influence of force field polarisation and cappingInfluence of C-5 substituted cytosine and related nucleoside analogs on the formation of benzo[a]pyrene diol epoxide-dG adducts at CG base pairs of DNA.A strategy for reducing gross errors in the generalized Born models of implicit solvation.Improved Generalized Born Solvent Model Parameters for Protein Simulations.Constrained Unfolding of a Helical Peptide: Implicit versus Explicit SolventsImproving the description of salt bridge strength and geometry in a Generalized Born model.Conformational sampling of peptides in cellular environments.Comparison of radii sets, entropy, QM methods, and sampling on MM-PBSA, MM-GBSA, and QM/MM-GBSA ligand binding energies of F. tularensis enoyl-ACP reductase (FabI).Conformational analysis of the carboxy-terminal tails of human beta-tubulin isotypes.Interactions between neuronal fusion proteins explored by molecular dynamicsRefinement of Generalized Born Implicit Solvation Parameters for Nucleic Acids and Their Complexes with Proteins.Mechanical stability of helical beta-peptides and a comparison of explicit and implicit solvent models.Molecular dynamics simulations and their application to four-stranded DNA.Molecular dynamics simulations of protein dynamics and their relevance to drug discovery.Biomolecularmodeling and simulation: a field coming of age.Poisson-Boltzmann Calculations: van der Waals or Molecular Surface?Thermal compaction of the intrinsically disordered protein tau: entropic, structural, and hydrophobic factors.An analytical approach to computing biomolecular electrostatic potential. I. Derivation and analysis.Accuracy of continuum electrostatic calculations based on three common dielectric boundary definitions.Uncovering specific electrostatic interactions in the denatured states of proteinsMultiscale Monte Carlo Sampling of Protein Sidechains: Application to Binding Pocket Flexibility.Quantitative analysis of Poisson-Boltzmann implicit solvent in molecular dynamics.Evaluating force field accuracy with long-time simulations of a β-hairpin tryptophan zipper peptide.Langevin-Debye model for nonlinear electrostatic screening of solvated ions.Peptoid conformational free energy landscapes from implicit-solvent molecular simulations in AMBER.Opening mechanism of adenylate kinase can vary according to selected molecular dynamics force field.Assessing the performance of MM/PBSA and MM/GBSA methods. 8. Predicting binding free energies and poses of protein-RNA complexesSampling large conformational transitions: adenylate kinase as a testing groundPoisson-Boltzmann Calculations: van der Waals or Molecular Surface?
P2860
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P2860
Secondary structure bias in generalized Born solvent models: comparison of conformational ensembles and free energy of solvent polarization from explicit and implicit solvation
description
2007 nî lūn-bûn
@nan
2007年の論文
@ja
2007年論文
@yue
2007年論文
@zh-hant
2007年論文
@zh-hk
2007年論文
@zh-mo
2007年論文
@zh-tw
2007年论文
@wuu
2007年论文
@zh
2007年论文
@zh-cn
name
Secondary structure bias in ge ...... xplicit and implicit solvation
@ast
Secondary structure bias in ge ...... xplicit and implicit solvation
@en
type
label
Secondary structure bias in ge ...... xplicit and implicit solvation
@ast
Secondary structure bias in ge ...... xplicit and implicit solvation
@en
prefLabel
Secondary structure bias in ge ...... xplicit and implicit solvation
@ast
Secondary structure bias in ge ...... xplicit and implicit solvation
@en
P2093
P2860
P356
P1476
Secondary structure bias in ge ...... xplicit and implicit solvation
@en
P2093
Carlos Simmerling
Daniel R Roe
Lauren Wickstrom
Viktor Hornak
P2860
P304
P356
10.1021/JP066831U
P407
P577
2007-01-27T00:00:00Z