Owner

NVIDIA-BioNeMo

8 indexed repositories · View on GitHub

bionemo-recipes
BioNeMo Recipes: For building and adapting AI models in drug discovery at scale

Python · 857 stars
bionemo-agent-toolkit
Turn any agent into a life science expert with NVIDIA BioNeMo skills.

Python · 462 stars
Proteina-Complexa
Generative model for protein binder design for protein and small molecule targets. Combines a pretrained flow-based generative model (bui...

Python · 432 stars
nvMolKit
A high-performance, GPU-accelerated library for key computational chemistry tasks, such as molecular similarity, conformer generation, an...

Cuda · 276 stars
KERMT
KERMT is a pretrained graph neural network model for molecular property prediction.

Python · 99 stars
BioNeMo-Inference-Runtime
Easy, fast, and memory-efficient structure prediction inference

Python · 60 stars
boltz-cp
Context Parallelism Code for Boltz-2

Python · 59 stars
cuik-molmaker
cuik-molmaker is a specialized package designed for molecular featurization, converting chemical structures into formats that can be effe...

C++ · 36 stars

Beginner friendly Everything

Open All

BatchMolGraph padding makes inference embeddings depend on batch composition Open

Difficulty 4/5 3-5 days Newbie friendliness 48/100

NVIDIA-BioNeMo/KERMT#31 · Opened Sep 17, 2026
Feature request: expose reproducibility metadata and full interface confidence for structure NIMs Open

Difficulty 5/5 Over a week Newbie friendliness 42/100

NVIDIA-BioNeMo/bionemo-agent-toolkit#33 · Opened Sep 15, 2026
v1.0 Cleanup Requirements Open

Low Priority

Difficulty 5/5 Over a week Newbie friendliness 25/100

NVIDIA-BioNeMo/nvMolKit#305 · Opened Sep 14, 2026
Enable clang-tidy builds again Open

Cleanup

Difficulty 3/5 1-2 days Newbie friendliness 45/100

NVIDIA-BioNeMo/nvMolKit#302 · Opened Sep 11, 2026
protenix-v2 has no end-to-end pipeline Open

Difficulty 5/5 Over a week Newbie friendliness 35/100

NVIDIA-BioNeMo/BioNeMo-Inference-Runtime#5 · 2 comments · Opened Sep 11, 2026
Numpy dtype changes pointer when pickling causing pointer comparison to fail in `compute_atom_dim` Open

Difficulty 4/5 3-5 days Newbie friendliness 48/100

NVIDIA-BioNeMo/cuik-molmaker#6 · Opened Sep 2, 2026
All-in-one ETKDG Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 38/100

NVIDIA-BioNeMo/nvMolKit#287 · Opened Sep 1, 2026
Investigate non-RDKit Clustering methods Open

enhancement

NVIDIA-BioNeMo/nvMolKit#286 · 1 assignee · Opened Sep 1, 2026
[ALERT] Access to NVIDIA's Self-Hosted Runners is Expiring Open

nvidia-runners

Difficulty 1/5 Under an hour Newbie friendliness 35/100

NVIDIA-BioNeMo/bionemo-recipes#1726 · Opened Aug 30, 2026
Explore lower precision for BFGS/FIRE/forcefields Open

enhancement

NVIDIA-BioNeMo/nvMolKit#266 · 1 assignee · Opened Aug 19, 2026
Flaky test: CUDA error: initialization error in DataLoader workers (esm2_native_te) Open

bug ESM2

Difficulty 4/5 3-5 days Newbie friendliness 48/100

NVIDIA-BioNeMo/bionemo-recipes#1698 · Opened Jul 29, 2026
Cyclicpeptide design Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

NVIDIA-BioNeMo/Proteina-Complexa#58 · Opened Jul 22, 2026
The generated proteins from the motif scaffolding example are bad Open

Difficulty 4/5 3-5 days Newbie friendliness 45/100

NVIDIA-BioNeMo/Proteina-Complexa#56 · 2 comments · Opened Jul 15, 2026
DDP finetuning relies on `find_unused_parameters=True`, masking dead pretrain-head parameters Open

Difficulty 4/5 3-5 days Newbie friendliness 48/100

NVIDIA-BioNeMo/KERMT#23 · Opened Jul 13, 2026
Cannot run on RTX 6000 / Blackwell (sm_120): pinned CUDA 12.6 + JAX 0.4.29 stack is incompatible Open

Difficulty 4/5 3-5 days Newbie friendliness 45/100

NVIDIA-BioNeMo/Proteina-Complexa#54 · Opened Jul 11, 2026
[Feature] Inference-side PTQ / weight-compression recipe for bio models (ESM-2 / Geneformer / Evo2) — wanted? where should it live? Open

Difficulty 5/5 Over a week Newbie friendliness 35/100

NVIDIA-BioNeMo/bionemo-recipes#1681 · Opened Jul 11, 2026
which PLINDER release matches plinder_valid_ids.txt? Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

NVIDIA-BioNeMo/Proteina-Complexa#52 · Opened Jul 6, 2026
Binder generation dies on FP64 torch.prod Open

Difficulty 2/5 1-3 hours Newbie friendliness 72/100

NVIDIA-BioNeMo/Proteina-Complexa#51 · Opened Jul 5, 2026
Contribution policy — third-party hosted inference endpoints in nim-skills Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

NVIDIA-BioNeMo/bionemo-agent-toolkit#5 · 2 comments · Opened Jul 4, 2026
[BUG] Evo2 doesnt work in Bionemo V3.0.0 Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 38/100

NVIDIA-BioNeMo/bionemo-recipes#1669 · 1 comment · Opened Jul 1, 2026
Question: Does changing target_hotspots affect binder generation? Open

Difficulty 4/5 3-5 days Newbie friendliness 38/100

NVIDIA-BioNeMo/Proteina-Complexa#50 · Opened Jun 29, 2026
Non-standard amino acid Open

Difficulty 5/5 Over a week Newbie friendliness 35/100

NVIDIA-BioNeMo/Proteina-Complexa#49 · Opened Jun 19, 2026
[Feature] Reflect vortex prefill improvements from PR 77 Open

Difficulty 5/5 Over a week Newbie friendliness 30/100

NVIDIA-BioNeMo/bionemo-recipes#1647 · Opened Jun 16, 2026
[Proteina-Complexa] Setup docs overstate required credentials and mislabel DATA_PATH Open

Difficulty 2/5 1-3 hours Newbie friendliness 72/100

NVIDIA-BioNeMo/Proteina-Complexa#48 · Opened Jun 15, 2026
[Proteina-Complexa] Skills lack a \"Limitations\" section (model scope is unstated) Open

Difficulty 1/5 1-3 hours Newbie friendliness 78/100

NVIDIA-BioNeMo/Proteina-Complexa#47 · Opened Jun 15, 2026
[Proteina-Complexa] `target_schema.md` field documentation is inaccurate Open

Difficulty 2/5 1-3 hours Newbie friendliness 84/100

NVIDIA-BioNeMo/Proteina-Complexa#46 · Opened Jun 15, 2026
[Proteina-Complexa] `complexa validate target` reports false failures for valid targets Open

Difficulty 2/5 1-3 hours Newbie friendliness 76/100

NVIDIA-BioNeMo/Proteina-Complexa#45 · Opened Jun 15, 2026
[Proteina-Complexa] Local finetune crashes: SkipNanGrad incompatible with the fp16 GradScaler Open

Difficulty 4/5 3-5 days Newbie friendliness 52/100

NVIDIA-BioNeMo/Proteina-Complexa#44 · Opened Jun 15, 2026
[Proteina-Complexa] Sweep inf_* configs crash at evaluate (generate/evaluate path mismatch) Open

Difficulty 3/5 1-2 days Newbie friendliness 68/100

NVIDIA-BioNeMo/Proteina-Complexa#43 · Opened Jun 15, 2026
[Proteina-Complexa] Fresh UV env installs a torchaudio incompatible with torch → import crash Open

Difficulty 1/5 Under an hour Newbie friendliness 88/100

NVIDIA-BioNeMo/Proteina-Complexa#42 · Opened Jun 15, 2026
[Feature] Support `.obsm` arrays in `SingleCellMemMapDataset` for spatial transcriptomics Open

Difficulty 5/5 Over a week Newbie friendliness 42/100

NVIDIA-BioNeMo/bionemo-recipes#1577 · Opened May 21, 2026
Missing complexa_cat.ckpt for fold class conditioned binder generation Open

Difficulty 3/5 1-2 days Newbie friendliness 52/100

NVIDIA-BioNeMo/Proteina-Complexa#37 · 4 comments · Opened May 13, 2026
RTX 5090 (sm_120) not supported - PyTorch cu126 incompatible with Blackwell architecture Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

NVIDIA-BioNeMo/Proteina-Complexa#36 · 1 comment · Opened May 13, 2026
MFU tracking: `pad_to_multiple_of` path inflates useful-work Σ(Lᵢ²) by the mock-sequence contribution Open

Difficulty 4/5 3-5 days Newbie friendliness 38/100

NVIDIA-BioNeMo/bionemo-recipes#1561 · Opened Apr 24, 2026
[Feature] Support loading & writing zarr files in scdl Open

Difficulty 4/5 3-5 days Newbie friendliness 52/100

NVIDIA-BioNeMo/bionemo-recipes#1560 · Opened Apr 22, 2026
Question about motif + ligand scaffolding Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

NVIDIA-BioNeMo/Proteina-Complexa#32 · 4 comments · Opened Apr 15, 2026
Question on GPU resources for training and inference Open

question

Difficulty 4/5 3-5 days Newbie friendliness 25/100

NVIDIA-BioNeMo/Proteina-Complexa#31 · Opened Apr 13, 2026
Missing train configs/yamls Open

Difficulty 3/5 1-2 days Newbie friendliness 48/100

NVIDIA-BioNeMo/Proteina-Complexa#30 · Opened Apr 9, 2026
Binder Redesign (as in Section 8) Open

question

Difficulty 4/5 3-5 days Newbie friendliness 45/100

NVIDIA-BioNeMo/Proteina-Complexa#26 · Opened Apr 7, 2026
Fork adapted to Mac users, now available Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

NVIDIA-BioNeMo/Proteina-Complexa#24 · Opened Apr 5, 2026
Residue numbers of motif Open

enhancement

Difficulty 2/5 1-3 hours Newbie friendliness 35/100

NVIDIA-BioNeMo/Proteina-Complexa#23 · 1 comment · Opened Apr 5, 2026
Masked target structure support Open

question

Difficulty 5/5 Over a week Newbie friendliness 25/100

NVIDIA-BioNeMo/Proteina-Complexa#9 · 4 comments · Opened Mar 19, 2026
Support and performance optimization for Hopper (H200) architecture? Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

NVIDIA-BioNeMo/boltz-cp#1 · 2 comments · Opened Mar 18, 2026
Wet lab data availability Open

question

Difficulty 5/5 Over a week Newbie friendliness 25/100

NVIDIA-BioNeMo/Proteina-Complexa#1 · 1 comment · Opened Mar 17, 2026
[BUG] Investigate non-determinism in evo2 recipe data preprocessing script and/or test Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 32/100

NVIDIA-BioNeMo/bionemo-recipes#1493 · 1 comment · Opened Mar 4, 2026
Molecules clustering code (PCA and K-means) for training datasets: Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

NVIDIA-BioNeMo/KERMT#3 · 4 comments · Opened Jan 6, 2026
make cuik-molmaker optional Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

NVIDIA-BioNeMo/KERMT#2 · 2 comments · Opened Nov 17, 2025
Remove CUDA Sync Workaround in Evo2 Training Script Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

NVIDIA-BioNeMo/bionemo-recipes#1301 · 3 comments · Opened Oct 31, 2025
[BUG] Incorrect documentation for Continuous Flow matching augmentation Open

bug

Difficulty 2/5 1-3 hours Newbie friendliness 55/100

NVIDIA-BioNeMo/bionemo-recipes#1272 · Opened Oct 24, 2025
[BUG] EVO2 7b_arc_longcontext can't use context parallelism (2 GPUs) for long sequence prediction: shape mismatch Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 35/100

NVIDIA-BioNeMo/bionemo-recipes#1268 · 2 reactions · Opened Oct 22, 2025

NVIDIA-BioNeMo

Get new issues in your inbox