Quantitative computer simulations of biomolecules: A snapshot (Q58881182)

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3 January 2020

title

Quantitative computer simulations of biomolecules: a snapshot (English)

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computational mathematics

3 January 2020

main subject

general chemistry

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3 January 2020

Wei Yang

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3 January 2020

Hugh Nymeyer

series ordinal

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3 January 2020

Bernd Berg

series ordinal

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3 January 2020

Rafael Brüschweiler

series ordinal

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3 January 2020

publication date

1 March 2008

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Journal of Computational Chemistry

3 January 2020

published in

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3 January 2020

volume

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3 January 2020

issue

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3 January 2020

page(s)

668-672

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Importance of the CMAP correction to the CHARMM22 protein force field: dynamics of hen lysozyme

3 January 2020

cites work

1 reference

Comparison of multiple Amber force fields and development of improved protein backbone parameters

21 January 2018

1 reference

Empirical force fields for biological macromolecules: overview and issues.

21 January 2018

1 reference

Molecular dynamics and NMR spin relaxation in proteins

21 January 2018

1 reference

Validation of Molecular Dynamics Simulations of Biomolecules Using NMR Spin Relaxation as Benchmarks: Application to the AMBER99SB Force Field.

21 January 2018

1 reference

Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules

21 January 2018

1 reference

Weak alignment NMR: a hawk-eyed view of biomolecular structure

21 January 2018

1 reference

Quantitative Molecular Ensemble Interpretation of NMR Dipolar Couplings without Restraints

21 January 2018

1 reference

A simple polarizable model of water based on classical Drude oscillators

21 January 2018

1 reference

CHARMM fluctuating charge force field for proteins: I parameterization and application to bulk organic liquid simulations.

21 January 2018

1 reference

CHARMM fluctuating charge force field for proteins: II protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model.

21 January 2018

1 reference

Polarizable Empirical Force Field for Alkanes Based on the Classical Drude Oscillator Model

21 January 2018

1 reference

Polarizable empirical force field for aromatic compounds based on the classical drude oscillator

21 January 2018

1 reference

Additive and Classical Drude Polarizable Force Fields for Linear and Cyclic Ethers

21 January 2018

1 reference

Determination of Electrostatic Parameters for a Polarizable Force Field Based on the Classical Drude Oscillator

21 January 2018

1 reference

A nonadditive methanol force field: bulk liquid and liquid-vapor interfacial properties via molecular dynamics simulations using a fluctuating charge model

21 January 2018

1 reference

Structure, thermodynamics, and liquid-vapor equilibrium of ethanol from molecular-dynamics simulations using nonadditive interactions

21 January 2018

1 reference

Revisiting the hexane-water interface via molecular dynamics simulations using nonadditive alkane-water potentials

21 January 2018

1 reference

Atomic Level Anisotropy in the Electrostatic Modeling of Lone Pairs for a Polarizable Force Field Based on the Classical Drude Oscillator

21 January 2018

1 reference

PDDG/PM3 and PDDG/MNDO: improved semiempirical methods

21 January 2018

1 reference

Extension of the PDDG/PM3 Semiempirical Molecular Orbital Method to Sulfur, Silicon, and Phosphorus

21 January 2018

1 reference

Influence of inter- and intramolecular hydrogen bonding on kemp decarboxylations from QM/MM simulations

21 January 2018

1 reference

Elucidation of hydrolysis mechanisms for fatty acid amide hydrolase and its Lys142Ala variant via QM/MM simulations

21 January 2018

1 reference

Specific Reaction Parametrization of the AM1/d Hamiltonian for Phosphoryl Transfer Reactions: H, O, and P Atoms

21 January 2018

1 reference

Reliable treatment of electrostatics in combined QM/MM simulation of macromolecules

21 January 2018

1 reference

Fast semiempirical calculations for nuclear magnetic resonance chemical shifts: a divide-and-conquer approach.

21 January 2018

1 reference

21 January 2018

1 reference

Validation of the binding site structure of the cellular retinol-binding protein (CRBP) by ligand NMR chemical shift perturbations

21 January 2018

1 reference

A Fast QM/MM (Quantum Mechanical/Molecular Mechanical) Approach to Calculate Nuclear Magnetic Resonance Chemical Shifts for Macromolecules

21 January 2018

1 reference

Prediction of Protein-Protein Association Rates from a Transition-State Theory

21 January 2018

1 reference

Calculation of protein-ligand binding affinities.

21 January 2018

1 reference

Comparison of calculation and experiment implicates significant electrostatic contributions to the binding stability of barnase and barstar

21 January 2018

1 reference

Electrostatic contribution to the binding stability of protein-protein complexes.

21 January 2018

1 reference

Immunophysical exploration of C3d-CR2(CCP1-2) interaction using molecular dynamics and electrostatics

21 January 2018

1 reference

Do electrostatic interactions destabilize protein-nucleic acid binding?

21 January 2018

1 reference

Effect of interaction potentials in diffusion‐influenced reactions with small reactive regions

21 January 2018

1 reference

Electrostatic recognition and induced fit in the kappa-PVIIA toxin binding to Shaker potassium channel.

21 January 2018

1 reference

Quantifying the kinetic paths of flexible biomolecular recognition

21 January 2018

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Optimal specificity and function for flexible biomolecular recognition

21 January 2018

1 reference

Multicanonical ensemble: A new approach to simulate first-order phase transitions

21 January 2018

1 reference

Replica Monte Carlo simulation of spin glasses.

21 January 2018

1 reference

Generalized ensemble and tempering simulations: a unified view.

21 January 2018

1 reference

Residual entropy of ordinary ice from multicanonical simulations

21 January 2018

1 reference

Toward the accurate first-principles prediction of ionization equilibria in proteins.

21 January 2018

1 reference

Resolution exchange simulation

21 January 2018

1 reference

Coupling of replica exchange simulations to a non-Boltzmann structure reservoir

21 January 2018

1 reference

Optimized parallel tempering simulations of proteins

21 January 2018

1 reference

Sampling enhancement for the quantum mechanical potential based molecular dynamics simulations: a general algorithm and its extension for free energy calculation on rugged energy surface

21 January 2018

1 reference

Efficient sampling of protein structures by model hopping.

21 January 2018

1 reference

Simulated scaling method for localized enhanced sampling and simultaneous "alchemical" free energy simulations: a general method for molecular mechanical, quantum mechanical, and quantum mechanical/molecular mechanical simulations

21 January 2018

1 reference

Synergistic approach to improve "alchemical" free energy calculation in rugged energy surface

21 January 2018

1 reference

Theoretical studies of transition states by the multioverlap molecular dynamics methods

21 January 2018

1 reference

Free-energy calculations with multiple Gaussian modified ensembles

21 January 2018

1 reference

On the convergence improvement in the metadynamics simulations: a Wang-Landau recursion approach

21 January 2018

1 reference

Replica exchange simulation of reversible folding/unfolding of the Trp-cage miniprotein in explicit solvent: on the structure and possible role of internal water

21 January 2018

1 reference

Protein folding kinetics and thermodynamics from atomistic simulations.

21 January 2018

1 reference

21 January 2018

Identifiers

DOI

10.1002/JCC.20819

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17708535%20AND%20SRC:MED&resulttype=core&format=json

3 January 2020

DBLP publication ID

journals/jcc/YangNZBB07

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17708535%20AND%20SRC:MED&resulttype=core&format=json