@platforma-open/milaboratories.antibody-variant-designer.block 1.0.1 → 1.2.1

package/block-pack/description.md

@@ -5,17 +5,43 @@ structure and its per-residue confidence from the [3D Structure
 Prediction](https://github.com/platforma-open/3d-structure-prediction) block,
 finds the chemical liability motifs, decides which of them are worth fixing
 from how solvent-exposed they are, proposes substitutions that the fold
-tolerates, and discards any proposal that fails to remove the target liability
-or that introduces a new one.
+tolerates, and discards any proposal that fails to remove the target liability.
+A humanization proposal is discarded when it introduces more new liabilities
+than the run allows, which is none by default.
+
+Three run modes are available. `liabilities` designs against the liability
+objective alone, the original behavior. `humanization` designs against the
+humanization objective alone, proposing substitutions at non-human framework
+positions, scored against a Sapiens human-repertoire prior read alongside
+AntiFold's own fold-tolerance matrices. `liabilities + humanization` runs both.
+In the combined mode the liability
+objective targets only liabilities that lie entirely inside a CDR, so the two
+objectives never propose against the same residue. Their variants are then
+combined into one dataset-wide rank that blends structural tolerance with a
+humanness score.
 
 Each surviving variant carries its rank within its parent antibody, the
 positions it changed, how tolerant the fold is at those positions, a
-binding-risk band, and a permanent marker that it is an unvalidated hypothesis.
-The result leaves the block as a fixed-column CSV for synthesis.
+humanness score when the humanization objective produced it, a binding-risk
+band, and a permanent marker that it is an unvalidated hypothesis. The
+humanness score is a raw OASis identity at a fixed tier — the fraction of the
+variant's 9-mer peptides also found in human antibody repertoires — not a
+calibrated OASis percentile, so it is not directly comparable to a calibrated
+percentile published elsewhere. The result leaves the block as a
+fixed-column CSV for synthesis, alongside a per-parent summary of which
+liabilities and which non-human positions were found and what was decided
+about each.
 
 Substitution tolerance comes from [AntiFold](https://doi.org/10.1093/bioadv/vbae202)
 per-position matrices, read once per antibody. No variant structure is
 predicted and no binding strength is estimated — binding is judged empirically
 in the wet lab.
 
+The Sapiens prior reads inside the same step as AntiFold rather than a step of
+its own. Both need torch, so a second step would still need its own GPU
+allocation on the same queue — a permanent cost paid on every run — to save at
+most a small fraction of that step's wall time, since the Sapiens checkpoint
+(≈4.4 MiB) is tiny next to AntiFold's (540.6 MiB). Splitting them buys no real
+concurrency the block doesn't already have to pay a second GPU job for.
+
 Supported formats: VHH, mAb, Fab, scFv. V-domain only.

package/block-pack/manifest.json

@@ -1 +1 @@
-{"schema":"v2","description":{"id":{"organization":"milaboratories","name":"antibody-variant-designer","version":"1.0.1"},"components":{"workflow":{"type":"workflow-v1","main":{"type":"relative","path":"main.plj.gz"}},"model":{"type":"relative","path":"model.json"},"ui":{"type":"relative","path":"ui.tgz"}},"meta":{"title":"Antibody Variant Designer","description":"Ranked antibody variant hypotheses that remove chemical liabilities.","longDescription":{"type":"relative","path":"description.md"},"changelog":{"type":"relative","path":"CHANGELOG.md"},"logo":{"type":"relative","path":"block-logo.png"},"url":"https://github.com/platforma-open/antibody-variant-designer","support":"mailto:support@milaboratories.com","tags":["antibody","developability","liabilities","protein-design"],"organization":{"name":"MiLaboratories Inc","url":"https://milaboratories.com/","logo":{"type":"relative","path":"organization-logo.png"}},"supportedPlatforms":["linux-x64","linux-aarch64","macosx-x64","macosx-aarch64","windows-x64"]},"featureFlags":{"supportsLazyState":true,"supportsPframeQueryRanking":true,"requiresUIAPIVersion":3,"requiresModelAPIVersion":2,"requiresCreatePTable":2,"requiresPFramesVersion":1001031,"requiresPFrameSpec":true,"requiresPFrame":true,"requiresDialog":true,"requiresColumnsCollection":true}},"timestamp":1789041548470,"files":[{"name":"main.plj.gz","size":503950,"sha256":"1A7643525114024C8319545D3FABDA9630C0D4979E13576CD0F22ACEB12931CF"},{"name":"model.json","size":511807,"sha256":"7440724016CDEEC2CF89060FFC61DAFD745C0D70669BA9AA60255FABA7AC1947"},{"name":"ui.tgz","size":3927560,"sha256":"7E8F96166A91086052388679ED9A04DB7E99C17D7A74A515E8D6514EBF6CBAD9"},{"name":"organization-logo.png","size":24439,"sha256":"FA71390C77C91E4B7FAAE5640D00F92F1E3F2869296F68B6040DD7CC549A50B5"},{"name":"description.md","size":1082,"sha256":"C2126F261CFFE0171EE38BAA1526F0E813361462279BB9317787952D14D1AE5D"},{"name":"CHANGELOG.md","size":88,"sha256":"8BDF88B95F10A0467C1C6694954F1CB9B74F5DE3227C5FF3B51B4A08E83B52AF"},{"name":"block-logo.png","size":21527,"sha256":"6BB33BAF0CD039549661B51AE490373BE60D1811EC71F5023400928293BC2427"}]}
+{"schema":"v2","description":{"id":{"organization":"milaboratories","name":"antibody-variant-designer","version":"1.2.1"},"components":{"workflow":{"type":"workflow-v1","main":{"type":"relative","path":"main.plj.gz"}},"model":{"type":"relative","path":"model.json"},"ui":{"type":"relative","path":"ui.tgz"}},"meta":{"title":"Antibody Variant Designer","description":"Ranked antibody variant hypotheses that remove chemical liabilities.","longDescription":{"type":"relative","path":"description.md"},"changelog":{"type":"relative","path":"CHANGELOG.md"},"logo":{"type":"relative","path":"block-logo.png"},"url":"https://github.com/platforma-open/antibody-variant-designer","support":"mailto:support@milaboratories.com","tags":["antibody","developability","liabilities","protein-design"],"organization":{"name":"MiLaboratories Inc","url":"https://milaboratories.com/","logo":{"type":"relative","path":"organization-logo.png"}},"supportedPlatforms":["linux-x64","linux-aarch64","macosx-x64","macosx-aarch64","windows-x64"]},"featureFlags":{"supportsLazyState":true,"supportsPframeQueryRanking":true,"requiresUIAPIVersion":3,"requiresModelAPIVersion":2,"requiresCreatePTable":2,"requiresPFramesVersion":1001031,"requiresPFrameSpec":true,"requiresPFrame":true,"requiresDialog":true,"requiresColumnsCollection":true},"kind":"@platforma-open/milaboratories.antibody-variant-designer.kind@1.0.0"},"timestamp":1790336917328,"files":[{"name":"main.plj.gz","size":513140,"sha256":"F5AC4853F93DC5D6185F8071CB4CA4CA750EA2568FA7C2385F62A77E84CB7C0A"},{"name":"model.json","size":566097,"sha256":"7B7CC858AF819496181D45F7094B8BFE38D9E7A15F79065B69ADB185851136A0"},{"name":"ui.tgz","size":6425641,"sha256":"6898C4AF52AEC633243C091841FC87CA441EF362275ADA8B3E1C74BBF784D7E7"},{"name":"organization-logo.png","size":24439,"sha256":"FA71390C77C91E4B7FAAE5640D00F92F1E3F2869296F68B6040DD7CC549A50B5"},{"name":"description.md","size":2764,"sha256":"C4CF9017F8C835413F91470400F1133B2306CF28B39DD7759718C893EB7D0C03"},{"name":"CHANGELOG.md","size":88,"sha256":"8BDF88B95F10A0467C1C6694954F1CB9B74F5DE3227C5FF3B51B4A08E83B52AF"},{"name":"block-logo.png","size":21527,"sha256":"6BB33BAF0CD039549661B51AE490373BE60D1811EC71F5023400928293BC2427"}]}