Difference between revisions of "Test System Repository"
Jump to navigation
Jump to search
MartinOlsson (talk | contribs) |
|||
| (42 intermediate revisions by 4 users not shown) | |||
| Line 4: | Line 4: | ||
To join a mailing list for a discussion of protein-ligand binding benchmarks, email michael.shirts at virginia.edu. If you have signed up previously, you can log into the discussion (password protected) at https://collab.itc.virginia.edu/portal/xlogin | To join a mailing list for a discussion of protein-ligand binding benchmarks, email michael.shirts at virginia.edu. If you have signed up previously, you can log into the discussion (password protected) at https://collab.itc.virginia.edu/portal/xlogin | ||
| − | = | + | = Specifications of the content of binding benchmark tests = |
| + | |||
| + | ''Current standards version is 0.5, dated Sept 27, 2013'' | ||
There will be three types of depositions for the binding benchmark test sets: | There will be three types of depositions for the binding benchmark test sets: | ||
| − | * | + | * [[System specifications]] |
| − | * | + | * [[Potential energy results]] |
| − | * | + | * [[Free energy results]] |
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | + | All tests consist of a system specification and at least one potential energy result from a specified software version. After that, multiple people can contribute free energy results for the same system specification and potential energy result, or contribute potential energy results of the system for different simulation codes. They also might propose a new potential energy result based on their own preferences for simulations of the system (different cutoffs, etc). Importantly, the "free energy results" should be an attempt to be independent of any such nonphysical approximations. | |
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
= Test Sets = | = Test Sets = | ||
| − | == | + | == Small Molecule Solvation Benchmark Sets == |
| − | * Small Molecule | + | * [[The Simple Small Molecule Solvation Benchmark Test Set]]: This test set was designed to test methods for computing hydration free energies of small molecules. It comprises a series of small molecules, parameter sets for three different software codes, and reference energies {{Cite|Paliwal2011}}. |
| + | * [http://www.escholarship.org/uc/item/6sd403pz FreeSolv (Mobley) Hydration Set]: This is an extensive (640+) molecule database of experimental and calculated hydration free energies for small neutral molecules. It includes GROMACS topology and coordinate files as well. | ||
== Host-Guest Binding == | == Host-Guest Binding == | ||
| − | |||
* Cucurbit[7]uril with benzene (partial charges artificially set to zero). This tests binding of a nonpolar guest that encounters little barrier to exiting a rigid host. | * Cucurbit[7]uril with benzene (partial charges artificially set to zero). This tests binding of a nonpolar guest that encounters little barrier to exiting a rigid host. | ||
* Cucurbit[7]uril with guest B5 {{Cite|Moghaddam2011}}. This tests binding of a bulky cationic guest that encounters a substantial energy barrier to exiting a rigid host. | * Cucurbit[7]uril with guest B5 {{Cite|Moghaddam2011}}. This tests binding of a bulky cationic guest that encounters a substantial energy barrier to exiting a rigid host. | ||
* Some guest binding beta-cyclodextrin. This would test binding to a much more flexible host. | * Some guest binding beta-cyclodextrin. This would test binding to a much more flexible host. | ||
| − | + | * Octa-acid with benzoic acid guest derivatives (from SAMPL4 and SAMPL5 blind prediction challenge){{Cite|Olsson2016}}. | |
== Protein-Ligand Binding == | == Protein-Ligand Binding == | ||
| − | The following test systems were proposed at the [[2012_Workshop_on_Free_Energy_Methods_in_Drug_Design| 2012 Workshop on Free Energy Methods in Drug Design]]. One proposal would be to include 5-10 ligands. However, we should discuss | + | The following test systems were proposed at the [[2012_Workshop_on_Free_Energy_Methods_in_Drug_Design| 2012 Workshop on Free Energy Methods in Drug Design]]. One proposal would be to include 5-10 ligands. However, we should discuss how many ligands are needed for numerical evaluation of methods. |
| − | * 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). [[Media:Minimal.tar.gz|GROMACS format minimal set of input files]]{{Cite|Boyce2009}}. (A full set of topology/coordinate files for this set is also available, though the minimal set is probably adequate for most purposes. If desired the full set is available [https://dl.dropboxusercontent.com/u/3409095/paper_support/fullL99AM102Q.tar.gz here (511MB)]) |
| − | * FKBP (rock solid, well-studied). [[Media:FKBP_AMBER_GAFF.tgz|AMBER parameterized input files in GROMACS format]] | + | * FKBP (rock solid, well-studied). Files in both GROMACS format and DESMOND-compatible .cms files, validated to give equivalent energies (up to energy calculation method differences) |
| + | ** [[Media:FKBP_AMBER_GAFF.tgz|AMBER parameterized input files in GROMACS format]] | ||
| + | ** [[Media:FKBP_desmond.tgz|The same input parameters converted into DESMOND 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). | ||
| − | * CCP model binding site | + | * CCP model binding site{{Cite|Rocklin2013}}. [[Media:CCP.zip|GROMACS format minimal set of input files]]. |
| + | * Absolute free energies - Diverse-ligands to bromodomain BRD4{{Cite|Aldeghi2016}}. Download a complete zip from: [http://dx.doi.org/10.5281/zenodo.57131 http://dx.doi.org/10.5281/zenodo.57131]. | ||
=References= | =References= | ||
| Line 111: | Line 45: | ||
{{Cite|Paliwal2011|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): 4115-4134, J. Chem. Theory Comput.|http://www.citeulike.org/group/14929/article/10029023}} | {{Cite|Paliwal2011|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): 4115-4134, J. Chem. Theory Comput.|http://www.citeulike.org/group/14929/article/10029023}} | ||
{{Cite|Moghaddam2011|Moghaddam,S., Yang,C., Rekharsky,M., Ko,Y.H., Kim,K., Inoue,Y., and Gilson,M.K. (2011) New Ultrahigh Affinity Host - Guest Complexes of Cucurbit[7]uril with Bicyclo[2.2.2]octane and Adamantane Guests: Thermodynamic Analysis and Evaluation of M2 Affinity Calculations. J.Am.Chem.Soc. 133:3570-3581.}} | {{Cite|Moghaddam2011|Moghaddam,S., Yang,C., Rekharsky,M., Ko,Y.H., Kim,K., Inoue,Y., and Gilson,M.K. (2011) New Ultrahigh Affinity Host - Guest Complexes of Cucurbit[7]uril with Bicyclo[2.2.2]octane and Adamantane Guests: Thermodynamic Analysis and Evaluation of M2 Affinity Calculations. J.Am.Chem.Soc. 133:3570-3581.}} | ||
| + | {{Cite|Boyce2009|Boyce, S. E., Mobley, D. L., Rocklin, G. J., Graves, A. P., Dill, K. A. and Shoichet, B. K. (2009) Predicting ligand binding affinity with alchemical free energy methods in a polar model binding site. J. Mol. Biol. 394:747-763.}} | ||
| + | {{Cite|Rocklin2013|Rocklin, G. J., Boyce, S. E., Fischer, M., Fish, I, Mobley, D. L., Shoichet, B. K., Dill, K. A. (2013) Blind prediction of charged ligand binding affinities in a model binding site. J. Mol. Biol. 425:4569-4583.}} | ||
| + | {{Cite|Aldeghi2016|Aldeghi, M., Heifetz, A., Bodkin, M. J., Knapp, S., Biggin, P.C (2016). Accurate calculation of the absolute free energy of binding for drug molecules. Chem Sci. 7:207-218.}} | ||
| + | {{Cite|Olsson2016| Olsson, M. A., Söderhjelm, P., Ryde U. (2016). J. Comp. Chem. 37:1589-1600.}} | ||
</references> | </references> | ||
Latest revision as of 09:55, 10 August 2016
Purpose of Test Sets
One of the biggest challenges to carefully validating and comparing free energy methods is defining and sharing well-defined test cases (molecular systems and force field parameters) with reliably known numerical results. If one is not sure of the value of the free energy dictated by the energy model and other physical parameters, it is impossible to make fine comparisons among methods. Additionally, different programs with different bookkeeping, or parameters that have been rounded in some way, can cause legitimate small differences between computed free energies, obscuring differences in the methods. The goal of this Repository is to help define and disseminate a stable set of test systems of varied nature and complexity for use by the free energy simulation community. Note that the free energies provided by these systems may not agree particularly well with experiment, but this is not necessary, because the purpose here is to test the numerical performance of the methods.
To join a mailing list for a discussion of protein-ligand binding benchmarks, email michael.shirts at virginia.edu. If you have signed up previously, you can log into the discussion (password protected) at https://collab.itc.virginia.edu/portal/xlogin
Specifications of the content of binding benchmark tests
Current standards version is 0.5, dated Sept 27, 2013
There will be three types of depositions for the binding benchmark test sets:
All tests consist of a system specification and at least one potential energy result from a specified software version. After that, multiple people can contribute free energy results for the same system specification and potential energy result, or contribute potential energy results of the system for different simulation codes. They also might propose a new potential energy result based on their own preferences for simulations of the system (different cutoffs, etc). Importantly, the "free energy results" should be an attempt to be independent of any such nonphysical approximations.
Test Sets
Small Molecule Solvation Benchmark Sets
- The Simple Small Molecule Solvation Benchmark Test Set: This test set was designed to test methods for computing hydration free energies of small molecules. It comprises a series of small molecules, parameter sets for three different software codes, and reference energies [1].
- FreeSolv (Mobley) Hydration Set: This is an extensive (640+) molecule database of experimental and calculated hydration free energies for small neutral molecules. It includes GROMACS topology and coordinate files as well.
Host-Guest Binding
- Cucurbit[7]uril with benzene (partial charges artificially set to zero). This tests binding of a nonpolar guest that encounters little barrier to exiting a rigid host.
- Cucurbit[7]uril with guest B5 [2]. This tests binding of a bulky cationic guest that encounters a substantial energy barrier to exiting a rigid host.
- Some guest binding beta-cyclodextrin. This would test binding to a much more flexible host.
- Octa-acid with benzoic acid guest derivatives (from SAMPL4 and SAMPL5 blind prediction challenge)[3].
Protein-Ligand Binding
The following test systems were proposed at the 2012 Workshop on Free Energy Methods in Drug Design. One proposal would be to include 5-10 ligands. However, we should discuss how many ligands are needed for numerical evaluation of methods.
- T4 Lysozyme, polar and apolar sites (methods should be able to get this). GROMACS format minimal set of input files[4]. (A full set of topology/coordinate files for this set is also available, though the minimal set is probably adequate for most purposes. If desired the full set is available here (511MB))
- FKBP (rock solid, well-studied). Files in both GROMACS format and DESMOND-compatible .cms files, validated to give equivalent energies (up to energy calculation method differences)
- 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[5]. GROMACS format minimal set of input files.
- Absolute free energies - Diverse-ligands to bromodomain BRD4[6]. Download a complete zip from: http://dx.doi.org/10.5281/zenodo.57131.
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): 4115-4134, J. Chem. Theory Comput. - Find at Cite-U-Like
- ↑ Moghaddam,S., Yang,C., Rekharsky,M., Ko,Y.H., Kim,K., Inoue,Y., and Gilson,M.K. (2011) New Ultrahigh Affinity Host - Guest Complexes of Cucurbit[7]uril with Bicyclo[2.2.2]octane and Adamantane Guests: Thermodynamic Analysis and Evaluation of M2 Affinity Calculations. J.Am.Chem.Soc. 133:3570-3581.
- ↑ Olsson, M. A., Söderhjelm, P., Ryde U. (2016). J. Comp. Chem. 37:1589-1600.
- ↑ Boyce, S. E., Mobley, D. L., Rocklin, G. J., Graves, A. P., Dill, K. A. and Shoichet, B. K. (2009) Predicting ligand binding affinity with alchemical free energy methods in a polar model binding site. J. Mol. Biol. 394:747-763.
- ↑ Rocklin, G. J., Boyce, S. E., Fischer, M., Fish, I, Mobley, D. L., Shoichet, B. K., Dill, K. A. (2013) Blind prediction of charged ligand binding affinities in a model binding site. J. Mol. Biol. 425:4569-4583.
- ↑ Aldeghi, M., Heifetz, A., Bodkin, M. J., Knapp, S., Biggin, P.C (2016). Accurate calculation of the absolute free energy of binding for drug molecules. Chem Sci. 7:207-218.