New Features: Open Source OpenMM relaxing and antigen trimming for memory efficiency. #26
Open
Lefrunila wants to merge 2 commits into
Open
New Features: Open Source OpenMM relaxing and antigen trimming for memory efficiency. #26Lefrunila wants to merge 2 commits into
Lefrunila wants to merge 2 commits into
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
I have added the option to relax using OpenMM, keeping the entire design pipeline Open Source.
I have also added a new feature: Antigen trimming, this allows inference to run only with epitope residues plus 5 neighbors per each. Including additional residues within a radius defined by the epitope's center of mass can be done too.
A restoration script is available to restore the trimmed antigen to its full original size after inference.
This significantly reduces inference time and memory usage, most antigens can be used for nanobody design with a 6 Gb GPU and 8 Gb for antibody design.
Note on Binding Pose Accuracy: In my test runs, I observed that the predicted binding poses sometimes differ significantly from the ground truth structures. Importantly, this occurs even with untrimmed antigens, suggesting it may be related to model parameterization or sampling rather than the trimming feature itself. I have included my test outputs
(test_runs_outputs.tar.gz)for the authors to review and investigate this behavior.test_runs_outputs.tar.gz