Repository containing pipelines developed for the SNAC-DB (Structural NANOBODY® VHH and Antibody Complex Database). SNAC-DB is ML-ready curation of the Protein Data Bank (PDB) for NANOBODY® VHH and antibody complex structures.
Small, fast, fully differentiable antibody Fv structure predictor in JAX. ~0.76M parameters, matches IgFold on CDR-H3, folds an Fv in ~0.8s on CPU.
This repository contains the NbX models for the re-ranking of nanobody–antigen binding poses.
Official repository for the OUP published paper: "Computational Design of a Predicted High-Affinity Humanised Nanobody against KRAS Switch-I". Includes the PIA-KRASv2-Nb sequence, 3D models, and validation data.
Llamanade (archived recovery) — Open-source nanobody humanization pipeline. Original repo by sangzhe was deleted along with all forks. Preserved from Software Heritage archive.
For NBsTem Webserver
Parallel antibody/nanobody repertoire NGS pipeline: FASTQ QC to IgBLAST annotation to clonal clustering to consensus reconstruction
Master thesis project, with aim to investigate tools that can potentially predict immunogenicity of therapeutic proteins. Further, the aim is to create a therapeutic profiler to predict immunogenicity of nanobodies, using the tools with best performance.
This repository contains codes for the regeneration of figures 3b and 3g in Tam, C., Kukimoto-Niino, M., Miyata-Yabuki, Y. et al. Targeting Ras-binding domain of ELMO1 by computational nanobody design. Commun Biol 6, 284 (2023).
Build a structural nanobody library from the PDB: mine RCSB for nanobody/VHH entries, split nanobody and antigen chains, renumber and superpose in headless PyMOL
Streamlit platform for antibody and nanobody sequence analysis with AbNatiV, NbForge, NbFrame, and NanoMelt.
CDR-selective resampling for Boltz-2: antibody-antigen interface ensembles, a differentiable CDR-epitope guidance potential, and a GPU-free evaluation suite.
novamab — independent third-party profile of a public API surface, by API Evangelist. Novamab (洛启生物) is a Shanghai-based clinical-stage biopharmaceutical company specializing in VHH (nanobody) antibody drug development for respiratory and inflammatory diseases such as asthma, COPD, and IBD.
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