https://github.com/rmeli/ifd

Induced Fit Docking Data Set
https://github.com/rmeli/ifd

Last synced: 22 days ago
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Induced Fit Docking Data Set

• Host: GitHub
• URL: https://github.com/rmeli/ifd
• Owner: RMeli
• Created: 2022-02-07T16:35:44.000Z (over 2 years ago)
• Default Branch: main
• Last Pushed: 2022-03-04T15:25:43.000Z (over 2 years ago)
• Last Synced: 2023-10-20T22:51:33.601Z (about 1 year ago)
• Language: Python
• Size: 2.07 MB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
# Induced Fit Docking Dataset

Reconstruct (partial) data set used to validate Induced Fit Docking (IFD).

> Sherman, W., Day, T., Jacobson, M. P., Friesner, R. A., & Farid, R. (2006). Novel procedure for modeling ligand/receptor induced fit effects. Journal of medicinal chemistry, 49(2), 534-553.

If you use the data in this repository, don't forget to cite the paper above.

## Notes

Visually, the poses in structures `3pgh` and `1cx2` (chain `A`) do not appear to correspond to the ones in Fig. 6 and Fig. 7. For `3pgh` the cognate ligand pose is the same, while the non-cognate ligand is different, which is not a problem since it will be sampled during docking.

Structures `1dba` and `1dm2` (*apo* structures) have been omitted on purpose because there is not ligand in the binding site (useful to automatically define the search space for docking).

## Dependencies

* [pandas](https://pandas.pydata.org/)

* [ProDy](http://prody.csb.pitt.edu/index.html)