AntiSite — antibody paratope prediction
0
11 commits
1 linked in READMEs
updated Jul 31, 2026
Live demo of AntiSite: modality dropout for antibody paratope prediction, with or without structure, from a single model.
docker pull angepapa/antisite:latestBoth tabs run the same checkpoint (antisite_paragraph.pt). The only difference is whether a
structure is supplied — modality dropout is what lets one set of weights serve both paths.
| Tab | Input | Notes |
|---|---|---|
| Sequence-only | VH + VL | Fused head receives a zero 3D tensor |
| 3D | Antibody PDB | ParaSurf extracts 256-d surface features first |
The example structures and sequences are drawn from the held-out Paragraph test set, so nothing shown here was seen during training of the demo checkpoint.
The Dockerfile clones AntiSite (pinned by ANTISITE_REF) and ParaSurf from GitHub rather than
vendoring copies, so the demo and the published CLI cannot drift apart. It bakes in every weight —
AntiSite checkpoints, ParaSurf, ProtT5 and ESM-2 — so nothing is downloaded at runtime and waking
from sleep is fast. To move the demo to a new release, bump ANTISITE_REF.
Requires GPU hardware — the 3D tab runs a 3D CNN over 15k–30k surface points per antibody, which is impractical on CPU.
bootstrap.py, requirements.txt and packages.txt are a tested fallback for running this Space
under sdk: gradio instead of sdk: docker, should the Docker SDK become unavailable. To switch,
change the sdk and app_port lines above to sdk: gradio / sdk_version: 4.44.1 /
python_version: "3.10" / app_file: app.py. app.py detects which mode it is in and needs no edit.
The fallback reproduces without an image build what the Dockerfile does at build time:
-DDESTLIB, so building
with our own LIBDIR is what makes it work without root. Verified to produce byte-identical
surfaces to a root install.pdb2pqr executable bit and downloads the frozen ParaSurf weights.OpenBabel there comes from openbabel-wheel rather than conda-forge. It is the same upstream 3.1.1,
and was checked to yield byte-identical atom properties, SMARTS matches and partial charges, so
ParaSurf's chemical features are unchanged.
AntiSite — antibody paratope prediction
0
11 commits
1 linked in READMEs
updated Jul 31, 2026
Live demo of AntiSite: modality dropout for antibody paratope prediction, with or without structure, from a single model.
docker pull angepapa/antisite:latestBoth tabs run the same checkpoint (antisite_paragraph.pt). The only difference is whether a
structure is supplied — modality dropout is what lets one set of weights serve both paths.
| Tab | Input | Notes |
|---|---|---|
| Sequence-only | VH + VL | Fused head receives a zero 3D tensor |
| 3D | Antibody PDB | ParaSurf extracts 256-d surface features first |
The example structures and sequences are drawn from the held-out Paragraph test set, so nothing shown here was seen during training of the demo checkpoint.
The Dockerfile clones AntiSite (pinned by ANTISITE_REF) and ParaSurf from GitHub rather than
vendoring copies, so the demo and the published CLI cannot drift apart. It bakes in every weight —
AntiSite checkpoints, ParaSurf, ProtT5 and ESM-2 — so nothing is downloaded at runtime and waking
from sleep is fast. To move the demo to a new release, bump ANTISITE_REF.
Requires GPU hardware — the 3D tab runs a 3D CNN over 15k–30k surface points per antibody, which is impractical on CPU.
bootstrap.py, requirements.txt and packages.txt are a tested fallback for running this Space
under sdk: gradio instead of sdk: docker, should the Docker SDK become unavailable. To switch,
change the sdk and app_port lines above to sdk: gradio / sdk_version: 4.44.1 /
python_version: "3.10" / app_file: app.py. app.py detects which mode it is in and needs no edit.
The fallback reproduces without an image build what the Dockerfile does at build time:
-DDESTLIB, so building
with our own LIBDIR is what makes it work without root. Verified to produce byte-identical
surfaces to a root install.pdb2pqr executable bit and downloads the frozen ParaSurf weights.OpenBabel there comes from openbabel-wheel rather than conda-forge. It is the same upstream 3.1.1,
and was checked to yield byte-identical atom properties, SMARTS matches and partial charges, so
ParaSurf's chemical features are unchanged.