Scope, inclusion rules, limitations
Сайт описывает genuinely generative ML tools для белков, антител и antibody-like therapeutics.
Что входит
- sequence generators
- inverse folding
- backbone / all-atom generators
- joint sequence–structure
- CDR/framework generators
- mutation/humanization workflows
Что не входит как generator
- обычный structure prediction
- docking
- MD
- affinity prediction
- developability prediction — только как dependency
Политика обновления
Last verified матрицы: 2026-08-13. Новые инструменты добавляются YAML-файлом и проходят validate.py.
Валидаторы и внешние модули
| Модуль | Роль | Input → output | Граница интерпретации | Source |
|---|---|---|---|---|
| AlphaFold2 / ColabFold | Structure/self-consistency validation | Sequence → monomer/complex structure | Not a generator in this catalogue | https://doi.org/10.1038/s41586-021-03819-2 |
| AlphaFold3 | Complex/interaction prediction | Sequences/ligands → complex | ipTM/pLDDT are not affinity | https://doi.org/10.1038/s41586-024-07487-w |
| RoseTTAFold2 / antibody-fine-tuned RF2 | Structure/complex prediction and self-consistency | Sequence + optional target/epitope → structure | Predictor component only | https://doi.org/10.1101/2023.05.24.542179 |
| tFold-Ab / tFold-Ag | Antibody and antibody–antigen complex prediction | Sequences + optional epitope → structure/complex | Predictors/rankers, not the generator itself | https://github.com/TencentAI4S/tfold |
| PyRosetta / Rosetta | Relaxation, energy and interface scoring | Structure/complex → relaxed structure/scores | Energy/ddG is not measured affinity | https://www.rosettacommons.org/software/license-and-download |
| DockQ / TM-score | Retrospective structural evaluation | Predicted/reference structures → metric | Evaluation only | https://github.com/bjornwallner/DockQ |
| Molecular dynamics | Conformational/interaction stress test | Selected complex → trajectories | MD does not generate validated binders by itself | NR |
| AbNatiV / BioPhi / OASis | Nativeness/humanness and humanization guidance | Antibody/VHH sequence → score / guided replacements | Scores do not equal clinical immunogenicity | https://doi.org/10.1038/s42256-023-00778-3 |
| CamSol / SAP-like aggregation metrics | Solubility/aggregation risk | Sequence/structure → risk score | Not a generator; assay confirmation required | https://doi.org/10.1038/srep01326 |
| Experimental binding/function assays | Ground-truth validation | Selected sequences → binding/function/developability data | Only this layer establishes measured affinity/function | NR |