Solvation Free Energy of Protonated Lysine: Molecular Dynamics Study
Explore this paper's citation graph
- Type
- article
- Published
- 2021-08-06
- Cited by
- 1
- References
- 40
- Access
- Open access
- OpenAlex
- https://openalex.org/W3190044890
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:237949262
Keywords
Solvation, Molecular dynamics, Thermodynamic integration, Free energy perturbation, Water model
References
- GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers
- Statistical Mechanics: Theory and Molecular Simulation
- High‐Temperature Equation of State by a Perturbation Method. I. Nonpolar Gases
- Proteins: A Theoretical Perspective of Dynamics, Structure, and Thermodynamics
- Statistical Mechanics of Fluid Mixtures
- Comparison of simple potential functions for simulating liquid water
- Nonlinear scaling schemes for Lennard-Jones interactions in free energy calculations.
- Good practices in free-energy calculations.
- Solvation free energy of amino acids and side-chain analogues.
- Comparison of efficiency and bias of free energies computed by exponential averaging, the Bennett acceptance ratio, and thermodynamic integration.
- Affinities of amino acid side chains for solvent water.
- Statistically optimal analysis of samples from multiple equilibrium states.
- Solvation free energies of amino acid side chain analogs for common molecular mechanics water models.
- The NIST Chemistry WebBook: A Chemical Data Resource on the Internet†
- Extremely precise free energy calculations of amino acid side chain analogs: Comparison of common molecular mechanics force fields for proteins
- THE MISSING TERM IN EFFECTIVE PAIR POTENTIALS
- Solvation energies of amino acid side chains and backbone in a family of host-guest pentapeptides.
- Free energy of hydrophobic hydration: A molecular dynamics study of noble gases in water
- Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids
- Solvation free energies and transfer free energies for amino acids from hydrophobic solution to water solution from a very simple residue model
Cited by
Related papers
- Nonpolar Solvation Free Energies of Protein-Ligand Complexes.
- Towards a transferable nonelectrostatic model for continuum solvation: The electrostatic and nonelectrostatic energy correction model
- Solvation free energy arithmetic for small organic molecules
- A New Semi-Explicit Solvation Model: Fast Physics for Better Results
- Prediction of aqueous free energies of solvation using coupled QM and MM explicit solvent simulations.
- Performance of molecular dynamics simulation for predicting of solvation free energy of neutral solutes in methanol
- Explicit Water Models Affect the Specific Solvation and Dynamics of Unfolded Peptides While the Conformational Behavior and Flexibility of Folded Peptides Remain Intact.
- Fast estimation of solvation free energies for diverse chemical species.
- Effect of conformational flexibility and solvation on receptor-ligand binding free energies.