Difference between revisions of "Test System Repository"
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* T4 Lysozyme, polar and apolar sites (methods should be able to get this) | * T4 Lysozyme, polar and apolar sites (methods should be able to get this) | ||
| − | * FKBP (rock solid, well-studied) [[Media:FKBP_AMBER_GAFF.tgz|AMBER parameterized input files in GROMACS format]] | + | * FKBP (rock solid, well-studied) |
| + | ** [[Media:FKBP_AMBER_GAFF.tgz|AMBER parameterized input files in GROMACS format]] | ||
* Trypsin (well studied, potential issues with sampling and charges it would be good for people to swing at) | * Trypsin (well studied, potential issues with sampling and charges it would be good for people to swing at) | ||
* DNA gyrase (from Vertex's data collection curated by Richard Dixon). | * DNA gyrase (from Vertex's data collection curated by Richard Dixon). | ||
Revision as of 21:03, 18 September 2013
One of the biggest problems in careful comparisons and validations of methods is the difficulty of trying to agree on a single number for the free energy. If one is not sure of the value of the free energy, fine comparisons of methods are very difficult. Additionally, different programs with different bookkeeping, or parameters that have been rounded in some way can have legitimate small differences in the free energies, obscuring differences in the methods.
Small Molecule Sets
The Simple Small Molecule Solvation Benchmark Test Set
This test set was published as part of Paliwal et al.[1] to allow testing differences between different free energy methods, and consists of a series of small molecules, parameter sets for three different software codes, and reference energies.
Ligand Binding Sets
Proposed Ligand Binding Set
Based on a discussion at the last 2012 Workshop on Free Energy Methods in Drug Design, a set of test systems was proposed. This test set is entirely designed to validate simulation methods and codes themselves, not to match experiment, which would require a much more complicated and diverse set. The preparation of this data set is still underway.
Proposed systems: (5-10 ligands per system)
- T4 Lysozyme, polar and apolar sites (methods should be able to get this)
- FKBP (rock solid, well-studied)
- Trypsin (well studied, potential issues with sampling and charges it would be good for people to swing at)
- DNA gyrase (from Vertex's data collection curated by Richard Dixon).
- CCP model binding site
References
- ↑ Paliwal, H and Shirts, M. R. (2011) An efficient method for the calculation of quantum mechanics/molecular mechanics free energies. J. Chem. Theory Comp. 7 (12), J. Chem. Theory Comput. - Find at Cite-U-Like