Force fields for protein simulations (Q35590728)

9 August 2017

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title

Force fields for protein simulations (English)

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9 August 2017

2

David A Case

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author name string

Jay W Ponder

series ordinal

1

1 reference

PubMed ID

14631816

9 August 2017

David A Case

series ordinal

2

1 reference

9 August 2017

1 January 2003

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Advances in Protein Chemistry

9 August 2017

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9 August 2017

66

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9 August 2017

27-85

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Absolute Binding Energies of Alkali-Metal Cation Complexes with Benzene Determined by Threshold Collision-Induced Dissociation Experiments and ab Initio Theory

9 August 2017

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

Incorporation of solvent effects into density functional calculations of molecular energies and geometries

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

Cooperative effects in simulated water

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

Quantum Calculation of Molecular Energies and Energy Gradients in Solution by a Conductor Solvent Model

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

Generalized born models of macromolecular solvation effects

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

The missing term in effective pair potentials

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

A Theory of Water and Ionic Solution, with Particular Reference to Hydrogen and Hydroxyl Ions

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

Calculations of proton-binding thermodynamics in proteins

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

Determining atom-centered monopoles from molecular electrostatic potentials. The need for high sampling density in formamide conformational analysis

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

CHARMM: A program for macromolecular energy, minimization, and dynamics calculations

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

Protein molecular dynamics with the generalized born/ACE solvent model

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

An evaluation of force-field treatments of aromatic interactions

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

Validation of the general purpose Tripos 5.2 force field

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

Solvent-accessible surfaces of proteins and nucleic acids

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

Continuum solvent molecular dynamics study of flexibility in interleukin-8

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

Implicit Solvation Models: Equilibria, Structure, Spectra, and Dynamics

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

Molecular dynamics simulations of the protein unfolding/folding reaction

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

Realistic simulations of native-protein dynamics in solution and beyond

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

Thole's interacting polarizability model in computational chemistry practice

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

Additivity principles in biochemistry

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

Universal solvation model based on conductor-like screening model

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

Identifying native-like protein structures using physics-based potentials

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

Cation-pi interactions in chemistry and biology: a new view of benzene, Phe, Tyr, and Trp

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

Evaluating CASP4 predictions with physical energy functions.

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

Distinguishing native conformations of proteins from decoys with an effective free energy estimator based on the OPLS all-atom force field and the Surface Generalized Born solvent model

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

The SGB/NP hydration free energy model based on the surface generalized born solvent reaction field and novel nonpolar hydration free energy estimators.

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

Exploring the energy landscape of a beta hairpin in explicit solvent

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

Alpha-helical stabilization by side chain shielding of backbone hydrogen bonds

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

Energy functions for peptides and proteins. I. Derivation of a consistent force field including the hydrogen bond from amide crystals.

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

Energy functions for peptides and proteins. II. The amide hydrogen bond and calculation of amide crystal properties.

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

Polarizable force fields

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

Pairwise solute descreening of solute charges from a dielectric medium

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

Parametrized Models of Aqueous Free Energies of Solvation Based on Pairwise Descreening of Solute Atomic Charges from a Dielectric Medium

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

Inter- and intramolecular potential for the N-formylglycinamide-water system. A comparison between theoretical modeling and empirical force fields

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

An ab Initio Quantum Mechanical Study of Hydrogen-Bonded Complexes of Biological Interest

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

Force Field Validation Using Protein Side Chain Prediction

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

Comparison of simple potential functions for simulating liquid water

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin.

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

Development of a polarizable force field for proteins via ab initio quantum chemistry: first generation model and gas phase tests

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

Theoretical studies of the structure and molecular dynamics of a peptide crystal.

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

COSMO: a new approach to dielectric screening in solvents with explicit expressions for the screening energy and its gradient

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

Multidimensional free-energy calculations using the weighted histogram analysis method

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

Novel generalized Born methods

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

Molecular dynamics of native protein. I. Computer simulation of trajectories

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

Accurate simulation of protein dynamics in solution

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

Consistent Force Field for Calculations of Conformations, Vibrational Spectra, and Enthalpies of Cycloalkane and n‐Alkane Molecules

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

Accelerated Poisson-Boltzmann calculations for static and dynamic systems

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

Structure and dynamics of ion transport through gramicidin A.

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

All-atom empirical potential for molecular modeling and dynamics studies of proteins

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

Structure and dynamics of liquid water with different long-range interaction truncation and temperature control methods in molecular dynamics simulations

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

Potentials of mean force between ionizable amino acid side chains in water

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

An atoms-in-molecules study of the genetically-encoded amino acids: I. Effects of conformation and of tautomerization on geometric, atomic, and bond properties

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

Generalized-ensemble algorithms for molecular simulations of biopolymers

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

Simulation of activation free energies in molecular systems

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

Optimized atomic radii for protein continuum electrostatics solvation forces.

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

Effective Born radii in the generalized Born approximation: the importance of being perfect

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

Potential energy functions: from consistent force fields to spectroscopically determined polarizable force fields

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

Molecular dynamics simulations of unfolding and refolding of a beta-hairpin fragment of protein G

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

Modern protein force fields behave comparably in molecular dynamics simulations

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

Consistent treatment of inter- and intramolecular polarization in molecular mechanics calculations

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

Polarizable Atomic Multipole Water Model for Molecular Mechanics Simulation

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

Coupling between folding and ionization equilibria: effects of pH on the conformational preferences of polypeptides.

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

A comparison of the CHARMM, AMBER and ECEPP potentials for peptides. II. Phi-psi maps for N-acetyl alanine N'-methyl amide: comparisons, contrasts and simple experimental tests

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

On the potential functions used in molecular dynamics simulations of ion channels

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

Implicit solvent models

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

Solution conformations and thermodynamics of structured peptides: molecular dynamics simulation with an implicit solvation model.

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

Effective atom volumes for implicit solvent models: comparison between Voronoi volumes and minimum fluctuation volumes

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

A precise analytical method for calculating the electrostatic energy of macromolecules in aqueous solution

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

Electrostatic contributions to molecular free energies in solution

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

The GROMOS Biomolecular Simulation Program Package

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

Electrostatic interactions in macromolecules: theory and applications

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

All-Atom Structure Prediction and Folding Simulations of a Stable Protein

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

Gaussian fluctuations and linear response in an electron transfer protein

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

Multipole correction of atomic monopole models of molecular charge distribution. I. Peptides

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

Improved simulation of liquid water by molecular dynamics

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

Theory and applications of the generalized Born solvation model in macromolecular simulations

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

Molecular and Atomic Polarizabilities: Thole's Model Revisited

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

AMBER: Assisted model building with energy refinement. A general program for modeling molecules and their interactions

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

An all atom force field for simulations of proteins and nucleic acids

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

Development of a simple, self-consistent polarizable model for liquid water

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

Cation-pi interactions in ligand recognition and catalysis

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

Native-like mean structure in the unfolded ensemble of small proteins

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

Simulation of folding of a small alpha-helical protein in atomistic detail using worldwide-distributed computing

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

Beta-hairpin folding simulations in atomistic detail using an implicit solvent model

1 reference

https://api.crossref.org/works/10.1016%2FS0065-3233%2803%2966002-X

7 January 2021

10.1016/S0065-3233(03)66002-X

Identifiers

DOI

1 reference

9 August 2017

1 reference

PubMed ID

14631816