Published July 4, 2016
| Version v1
Dataset
Open
Aldeghi et al. Files for absolute free energy calculations in gromacs.
- 1. University of Oxford
- 2. Evotec Ltd
Description
These are the files for performing absolute free energy calculations using gromacs as reported in "Accurate calculation of the absolute free energy of binding for drug molecules. Aldeghi M, Heifetz A, Bodkin MJ, Knapp S, Biggin PC.
Chem Sci. 2016 Jan 14;7(1):207-218. DOI: 10.1039/C5SC02678D"
The files should prove useful for anyone wishing to try out their own methodology for comparison purposes or even just to repeat the work on a known dataset. The data is presented as a zip archive that should unpack into a directory called "Aldeghi-et-al-chemical-science-2016". There are four sub-directories in there and a README.txt file which should explain the details of the data.
Notes
1. All .xvg files are in their own XVG folder (the example_xvg_files folder in "crystal/ligand1/complex" is not needed/relevant).
2. In xvg/docking the scripts cp_tmp.sh and stride_all.sh were just used by us locally and are not useful here.
3. The mixture of "L" or "l" is a "dropbox feature" ! and does not mean anything.
4. The xvg folder has both the ligand numerical IDS and name as the folder name rather than just the ligand number (Ie "Ligand1_BI2356" rather than just "Ligand1").
Files
Aldeghi-et-al-chemical-science-2016.zip
Files
(140.2 MB)
| Name | Size | Download all |
|---|---|---|
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md5:3e8bf2202d864fb76f5c10063c410678
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140.2 MB | Preview Download |
Additional details
Related works
- Is supplement to
- 10.1039/C5SC02678D (DOI)
References
- Accurate calculation of the absolute free energy of binding for drug molecules. Aldeghi M, Heifetz A, Bodkin MJ, Knapp S, Biggin PC.
- Chem Sci. 2016 Jan 14;7(1):207-218.