DockM8

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# DockM8 Feature Request ## Description Add ability to generate protein conformational ensemble automatically to then use in ensemble docking. ## Problem Statement Several conformations may not be available for...

Tonylac77

Hi developers, a nice implementation would be [LigGrep](https://github.com/durrantlab/liggrep). I can immagine to add the user defined filter as addition to the pose_selection protocol.

HiteSit

Hi developers, DockM8 (or a low-computational-power version of it) could be integrated as a scoring function for a [[Thomson Sampling approach by PatWalters](https://github.com/PatWalters/TS)](https://github.com/PatWalters/TS) or [[Thomson Sampling Enhanced](https://github.com/WIMNZhao/TS_Enhanced)](https://github.com/WIMNZhao/TS_Enhanced). This integration could...

HiteSit

Hi developers, A nice feature that can be integrated is rescoring under dynamic conditions through MMPBSA/MMGBSA. One approach I can envision is to rescore only the top subset of best...

HiteSit

IF-SitePred : [github](https://github.com/oxpig/binding-sites) P2Rank : [github](https://github.com/rdk/p2rank)

Tonylac77

Allow for active compound retrieval from CHEMBL and other datasets for decoy generation

1

Collect the known actives (positive controls) for retrospective analysis. For a given target, these can be found in the scientific literature, patent literature or public databases such as IUPHAR/BPS[114](https://www.nature.com/articles/s41596-021-00597-z#ref-CR114), ChEMBL[115](https://www.nature.com/articles/s41596-021-00597-z#ref-CR115)...

Tonylac77

- [x] [GenScore](https://github.com/sc8668/GenScore): A scoring framework for predicting protein-ligand binding affinity. - [x] [ITScoreAff](http://huanglab.phys.hust.edu.cn/ITScoreAff/): iterative knowledge-based scoring function for protein-ligand interactions by considering binding affinity information - [x] DLIGAND2 -...

Tonylac77

Improve software installation so that when a tool is selected, it is automatically downloaded if not present in the software directory

Tonylac77

- [ ] https://github.com/dptech-corp/Uni-Dock - [ ] https://github.com/schrojunzhang/KarmaDock - [x] https://github.com/molecularmodelinglab/plantain - [x] FABind+ - [x] PANTHER - [ ] rdock : via bioconda rdock then https://rdock.github.io/how-to-run-rdock-in-parallel/

Tonylac77

- [ ] Score / MW - [x] Strain energy - [ ] https://tldr.docking.org/start/strain/STRAIN.tar.gz - [ ] Lipophilicity - [ ] Burial ? - [ ] Interaction Filtering - [...

Tonylac77