Extremely precise free energy calculations of amino acid side chain analogs: Comparison of common molecular mechanics force fields for proteins
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Summary
This work calculates the free energy of hydration of 15 amino acid side chain analogs derived from recent versions of the OPLS-AA, CHARMM, and AMBER parameter sets in TIP3P water using thermodynamic integration and achieves a high degree of statistical precision.
- Type
- article
- Published
- 2003-08-28
- Cited by
- 609
- References
- 90
- Access
- Open access
- OpenAlex
- https://openalex.org/W2047631698
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:32892734
Keywords
Force field (fiction), Chemistry, Side chain, Molecule, Thermodynamic integration
References
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- Rattle: A “velocity” version of the shake algorithm for molecular dynamics calculations
- Application of the RESP Methodology in the Parametrization of Organic Solvents
- Free Energies of Hydration and Pure Liquid Properties of Hydrocarbons from the OPLS All-Atom Model
- The lag between the Hamiltonian and the system configuration in free energy perturbation calculations
- The nature of the accessible and buried surfaces in proteins.
- Multiconfiguration thermodynamic integration
- Determination of equilibrium properties of biomolecular systems using multidimensional adaptive umbrella sampling
- Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling
- A molecular dynamics simulation study of chloroform
- Density of states simulations of proteins
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- Direct Mixing of Atomistic Solutes and Coarse-Grained Water.
- Efficient Solvation Free Energy Calculations of Amino Acid Analogs by Expanded Ensemble Molecular Simulation.
- Efficient Strategy for the Calculation of Solvation Free Energies in Water and Chloroform at the Quantum Mechanical/Molecular Mechanical Level
- Hydration peculiarities of graphene oxides with multiple oxidation degrees.
- Use of Polynomial Interpolation to Reduce Bias and Uncertainty of Free Energy Estimates via Thermodynamic Integration
- Computational Methods for Calculation of Ligand-Receptor Binding Affinities Involving Protein and Nucleic Acid Complexes
- The effect of fluorination on the physical properties and the free energies of hydration of 1-alcohols
- Toward high-throughput predictions of the hydration free energies of small organic molecules from first principles
- Calculation of binding free energies.
- Molecular dynamics simulation of water permeation through the alpha-hemolysin channel
- Using Bayes' Theorem for Free Energy Calculations
- Complementary use of computer simulations and molecular-thermodynamic theory to model surfactant and solubilizate self-assembly
- Thermodynamic properties for applications in chemical industry via classical force fields.
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- A computer simulation and molecular-thermodynamic framework to model the micellization of ionic branched surfactants in aqueous solution
- Frontiers in free‐energy calculations of biological systems
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