Skip to content

Add notebook for running OpenFE with OF3 generated inputs #266

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
IAlibay merged 9 commits into from
Nov 24, 2025
Merged

Add notebook for running OpenFE with OF3 generated inputs #266

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
9 commits
Select commit Hold shift + click to select a range
5ecac61
Add notebook for running SepTop with OF3 generated inputs
hannahbaumann Nov 19, 2025
d5ccf21
Merge branch 'main' into of3_septop_example
IAlibay Nov 20, 2025
3b06de5
Add openfold3 outputs
hannahbaumann Nov 20, 2025
1dbcd36
Remove other loc
hannahbaumann Nov 20, 2025
e0db1f0
Merge branch 'of3_septop_example' of github.com:OpenFreeEnergy/Exampl…
hannahbaumann Nov 20, 2025
8ad344c
Updating OpenFold to OpenFE notebook
IAlibay Nov 21, 2025
2045983
Apply suggestions from code review
IAlibay Nov 21, 2025
557e1fc
fixes
IAlibay Nov 21, 2025
18ed184
Review comments
IAlibay Nov 24, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
Binary file added cookbook/assets/OFE-color-horizontal.png
View file
Open in desktop
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
3,090 changes: 3,090 additions & 0 deletions cookbook/assets/of3_output/lig_ejm_31_seed_42_sample_1_model.pdb
View file
Open in desktop

Large diffs are not rendered by default.

3,092 changes: 3,092 additions & 0 deletions cookbook/assets/of3_output/lig_ejm_42_seed_42_sample_1_model.pdb
View file
Open in desktop

Large diffs are not rendered by default.

3,094 changes: 3,094 additions & 0 deletions cookbook/assets/of3_output/lig_ejm_43_seed_42_sample_1_model.pdb
View file
Open in desktop

Large diffs are not rendered by default.

3,094 changes: 3,094 additions & 0 deletions cookbook/assets/of3_output/lig_ejm_46_seed_42_sample_1_model.pdb
View file
Open in desktop

Large diffs are not rendered by default.

3,096 changes: 3,096 additions & 0 deletions cookbook/assets/of3_output/lig_ejm_47_seed_42_sample_1_model.pdb
View file
Open in desktop

Large diffs are not rendered by default.

3,098 changes: 3,098 additions & 0 deletions cookbook/assets/of3_output/lig_ejm_48_seed_42_sample_1_model.pdb
View file
Open in desktop

Large diffs are not rendered by default.

3,092 changes: 3,092 additions & 0 deletions cookbook/assets/of3_output/lig_ejm_50_seed_42_sample_1_model.pdb
View file
Open in desktop

Large diffs are not rendered by default.

3,096 changes: 3,096 additions & 0 deletions cookbook/assets/of3_output/lig_jmc_23_seed_42_sample_1_model.pdb
View file
Open in desktop

Large diffs are not rendered by default.

3,096 changes: 3,096 additions & 0 deletions cookbook/assets/of3_output/lig_jmc_27_seed_42_sample_1_model.pdb
View file
Open in desktop

Large diffs are not rendered by default.

3,096 changes: 3,096 additions & 0 deletions cookbook/assets/of3_output/lig_jmc_28_seed_42_sample_1_model.pdb
View file
Open in desktop

Large diffs are not rendered by default.

Binary file added cookbook/assets/tyk2.png
View file
Open in desktop
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
808 changes: 808 additions & 0 deletions cookbook/assets/tyk2_ligands.sdf
View file
Open in desktop

Large diffs are not rendered by default.

1,065 changes: 1,065 additions & 0 deletions cookbook/openfold3_to_openfe.ipynb
View file
Open in desktop

Large diffs are not rendered by default.

Loading