Advances in Free-Energy Calculations Based on Classical Molecular Dynamics Simulations
Niels Hansen
- 01 Jan 2014
3
About: The article was published on 01 Jan 2014. and is currently open access. The article focuses on the topics: Molecular dynamics.
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Citations
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References
Prediction of Absolute Solvation Free Energies using Molecular Dynamics Free Energy Perturbation and the OPLS Force Field.
TL;DR: This work uses explicit solvent molecular dynamics free energy perturbation to predict the absolute solvation free energies of a set of 239 small molecules, spanning diverse chemical functional groups commonly found in drugs and drug-like molecules and shows that predictions can be improved by using a semiempirical charge assignment method with an implicit bond charge correction.
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Fast, efficient generation of high‐quality atomic charges. AM1‐BCC model: I. Method
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Automation of the CHARMM General Force Field (CGenFF) II: Assignment of Bonded Parameters and Partial Atomic Charges
TL;DR: Algorithms for the assignment of parameters and charges for the CHARMM General Force Field (CGenFF) are presented and a "penalty score" is returned for every bonded parameter and charge, allowing the user to quickly and conveniently assess the quality of the force field representation of different parts of the compound of interest.
The Many Roles of Computation in Drug Discovery
TL;DR: An overview is given on the diverse uses of computational chemistry in drug discovery, with particular emphasis on virtual screening, de novo design, evaluation of drug-likeness, and advanced methods for determining protein-ligand binding.
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