Proteina-Complexa

NVIDIA Clara (ヘルスケア AI 統合プラットフォーム)
│
├── 【創薬・デジタルバイオ】 BioNeMo
│         ├── Proteina-Complexa (タンパク質バインダー設計)    <-- ここ
│         ├── 基盤モデル (ESM-2nv, MolMIM, OpenFold 等)
│         └── BioNeMo NIM (AI デプロイ用マイクロサービス)
│
├── 【ゲノム解析】 NVIDIA Parabricks
│         └── DNA/RNA 配列解析、バリアントコール高速化
│
├── 【医療機器・手術ロボ】 NVIDIA Holoscan
│         ├── 手術支援、内視鏡ビデオ、超音波のリアルタイム AI 処理
│         └── IGX / AGX (医療用エッジコンピューティング基盤)
│
├── 【医用画像・放射線】 MONAI (Medical Open Network for AI)
│         └── 読影支援、セグメンテーション、アノテーション支援
│
├── 【医療現場・スマート病院】 Clara Guardian
│         └── 病院内の患者モニタリング、音声アシスタント
│
└── 【共通ライブラリ】 nvMolKit / CUDA-X
           └── 分子解析やシミュレーションの高速化

[saber@rockylinux9 ~]$ cat /etc/redhat-release
Rocky Linux release 9.7 (Blue Onyx)
 
[saber@rockylinux9 ~]$ git clone https://github.com/NVIDIA-Digital-Bio/Proteina-Complexa
[saber@rockylinux9 ~]$ cd Proteina-Complexa
 
[saber@rockylinux9 Proteina-Complexa]$ ./env/build_uv_env.sh
==============================================
  Proteina-Complexa - Public Environment Builder
==============================================
Project directory: /home/saber/Proteina-Complexa
Install directory: /home/saber/Proteina-Complexa
Python version: 3.12
Prompt name: complexa
Full install: true
 
[1/8] Installing uv...
downloading uv 0.11.7 x86_64-unknown-linux-gnu
installing to /home/saber/.local/bin
  uv
  uvx
everything's installed!
 :
 :
==============================================
  Installation Complete!
==============================================
 
To activate the environment:
  source /home/saber/Proteina-Complexa/.venv/bin/activate
 
To verify installation:
  python -c "import torch; print(f'PyTorch: {torch.__version__}, CUDA: {torch.cuda.is_available()}')"
 
Note: Foldseek and MMseqs2 are not included in the public build.
Install them separately if needed:
  wget https://mmseqs.com/foldseek/foldseek-linux-gpu.tar.gz
  wget https://mmseqs.com/latest/mmseqs-linux-gpu.tar.gz
 
[saber@rockylinux9 Proteina-Complexa]$
(テスト)
[saber@rockylinux9 Proteina-Complexa]$ which python
/usr/bin/python
 
[saber@rockylinux9 Proteina-Complexa]$ source /home/saber/Proteina-Complexa/.venv/bin/activate
 
(complexa) [saber@rockylinux9 Proteina-Complexa]$ which python
~/Proteina-Complexa/.venv/bin/python
 
(complexa) [saber@rockylinux9 Proteina-Complexa]$ python -c "import torch; print(f'PyTorch: {torch.__version__}, CUDA: {torch.cuda.is_available()}')"
PyTorch: 2.7.0+cu126, CUDA: True
(complexa) [saber@rockylinux9 Proteina-Complexa]$

[saber@rockylinux9 ~]$ cd Proteina-Complexa/
 
[saber@rockylinux9 Proteina-Complexa]$ source .venv/bin/activate
 
(complexa) [saber@rockylinux9 Proteina-Complexa]$ complexa download
ℹ Working directory: /home/saber/Proteina-Complexa
 
 
lqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqk
x                                                                   x
x          🧬  Protein Foundation Models - Setup Wizard  🧬         x
x                                                                   x
mqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqj
 
 
qqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqq
  Current Installation Status
qqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqq
 
  Complexa Models (Required):
    Complexa (Protein): ○ Missing (ckpts/):
      ✗ complexa.ckpt (flow matching model)
      ✗ complexa_ae.ckpt (autoencoder)
    Complexa (Ligand):  ○ Missing (ckpts/):
      ✗ complexa_ligand.ckpt (flow matching model)
      ✗ complexa_ligand_ae.ckpt (autoencoder)
    Complexa (AME):     ○ Missing (ckpts/):
      ✗ complexa_ame.ckpt (flow matching model)
      ✗ complexa_ame_ae.ckpt (autoencoder)
 
  Core Models:
    ProteinMPNN:     ○ Missing (community_models/ProteinMPNN/):
      ✗ ca_model_weights/v_48_002.pt
      ✗ ca_model_weights/v_48_010.pt
      ✗ ca_model_weights/v_48_020.pt
      ✗ vanilla_model_weights/v_48_002.pt
      ✗ vanilla_model_weights/v_48_010.pt
      ✗ vanilla_model_weights/v_48_020.pt
      ✗ vanilla_model_weights/v_48_030.pt
    LigandMPNN:      ○ Missing (community_models/LigandMPNN/model_params/):
      ✗ proteinmpnn_v_48_002.pt
      ✗ proteinmpnn_v_48_010.pt
      ✗ proteinmpnn_v_48_020.pt
      ✗ proteinmpnn_v_48_030.pt
      ✗ ligandmpnn_v_32_005_25.pt
      ✗ ligandmpnn_v_32_010_25.pt
      ✗ ligandmpnn_v_32_020_25.pt
      ✗ ligandmpnn_v_32_030_25.pt
      ✗ per_residue_label_membrane_mpnn_v_48_020.pt
      ✗ global_label_membrane_mpnn_v_48_020.pt
      ✗ solublempnn_v_48_002.pt
      ✗ solublempnn_v_48_010.pt
      ✗ solublempnn_v_48_020.pt
      ✗ solublempnn_v_48_030.pt
      ✗ ligandmpnn_sc_v_32_002_16.pt
    AlphaFold2:      ○ Missing (community_models/ckpts/AF2/):
      ✗ params_model_1.npz
      ✗ params_model_1_ptm.npz
      ✗ params_model_1_multimer_v3.npz
      ✗ params_model_2.npz
      ✗ params_model_2_ptm.npz
      ✗ params_model_2_multimer_v3.npz
      ✗ params_model_3.npz
      ✗ params_model_3_ptm.npz
      ✗ params_model_3_multimer_v3.npz
      ✗ params_model_4.npz
      ✗ params_model_4_ptm.npz
      ✗ params_model_4_multimer_v3.npz
      ✗ params_model_5.npz
      ✗ params_model_5_ptm.npz
      ✗ params_model_5_multimer_v3.npz
    ESM2:            ○ Not installed (community_models/ckpts/ESM2/)
    RF3:             ○ Missing (community_models/ckpts/RF3/):
      ✗ rf3_foundry_01_24_latest_remapped.ckpt
 
What would you like to download?
 
  Complexa Models:
  p) Download Complexa Protein weights (protein binder design)
  l) Download Complexa Ligand weights (ligand binder design)
  e) Download Complexa AME weights (enzyme/motif scaffolding)
  a) Download all Complexa weights (protein + ligand + AME)
 
  Community Models:
  1) Download all community weights (ProteinMPNN + LigandMPNN + AF2 + ESM2 + RF3)
  2) Download ProteinMPNN weights only (~50MB)
  3) Download LigandMPNN weights only (~500MB)
  4) Download AlphaFold2 weights only (~5GB)
  5) Download ESM2 weights only (~2.6GB) [requires HF_TOKEN if rate limited]
  6) Download RoseTTAFold3 weights (~2.5GB)
  7) Download everything (all Complexa + community)
 
  Other:
  s) Check installation status
  q) Quit
 
Enter your choice [p, l, e, a, 1-7, s, q]: a    <-- 試しに 「Complexa Models」のにダウンロード
 
qqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqq
  Downloading Complexa Weights
qqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqq
 
→ Creating ckpts directory...
→ Downloading complexa.ckpt (flow matching model)...
 :
 :
(complexa) [saber@rockylinux9 Proteina-Complexa]$ ls -lh ckpts/
total 18G
-rw-r--r--. 1 saber saber 3.9G Mar 16 02:00 complexa_ae.ckpt
-rw-r--r--. 1 saber saber 3.9G Mar 16 02:05 complexa_ame_ae.ckpt
-rw-r--r--. 1 saber saber 1.7G Mar 16 02:05 complexa_ame.ckpt
-rw-r--r--. 1 saber saber 2.8G Mar 16 02:00 complexa.ckpt
-rw-r--r--. 1 saber saber 3.9G Mar 16 02:07 complexa_ligand_ae.ckpt
-rw-r--r--. 1 saber saber 1.7G Mar 16 02:08 complexa_ligand.ckpt
(complexa) [saber@rockylinux9 Proteina-Complexa]$

(complexa) [saber@rockylinux9 Proteina-Complexa]$ vi .env
LOCAL_CODE_PATH=/path/to/Proteina-Complexa
LOCAL_DATA_PATH=/path/to/PFM_data
  ↓
LOCAL_CODE_PATH=/home/saber/Proteina-Complexa
LOCAL_DATA_PATH=/home/saber/PFM_data
 
(complexa) [saber@rockylinux9 Proteina-Complexa]$ mkdir /home/saber/PFM_data

(complexa) [saber@rockylinux9 Proteina-Complexa]$ complexa validate design configs/search_binder_local_pipeline.yaml
 
======================================================================
  🔍 Validation Report: Design Pipeline
  Config: configs/search_binder_local_pipeline.yaml
======================================================================
 
  ⚠ Warnings (2):
    ⚠ Foldseek
      File not found: /home/saber/Proteina-Complexa/.venv/bin/foldseek
      💡 Ensure the file exists at the specified path
    ⚠ Shape complementarity (sc)
      File not found: /home/saber/Proteina-Complexa/env/docker/internal/sc
      💡 Ensure the file exists at the specified path
 
  ✓ Passed (5):
    ✓ .env file: Found
    ✓ DATA_PATH: /home/saber/PFM_data
    ✓ Config file: configs/search_binder_local_pipeline.yaml
    ✓ Complexa checkpoint: ckpts/complexa.ckpt
    ✓ Autoencoder checkpoint: ckpts/complexa_ae.ckpt
 
qqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqq
  ⚠ Validation passed with warnings
======================================================================
 
(complexa) [saber@rockylinux9 Proteina-Complexa]$

(complexa) [saber@rockylinux9 Proteina-Complexa]$ git clone https://github.com/cytokineking/FreeBindCraft
(complexa) [saber@rockylinux9 Proteina-Complexa]$ ls -l FreeBindCraft/functions/
 :
-rw-r--r--. 1 saber saber   877904 Apr 22 01:07 dssp
 :
-rwxr-xr-x. 1 saber saber   934480 Apr 22 01:07 sc
 :
(complexa) [saber@rockylinux9 Proteina-Complexa]$

(complexa) [saber@rockylinux9 Proteina-Complexa]$ wget https://github.com/steineggerlab/foldseek/releases/download/10-941cd33/foldseek-linux-gpu.tar.gz
(complexa) [saber@rockylinux9 Proteina-Complexa]$ tar xf foldseek-linux-gpu.tar.gz
(complexa) [saber@rockylinux9 Proteina-Complexa]$ ls -l foldseek/bin/foldseek
-rwxr-xr-x. 1 saber saber 735401248 Jan 19  2025 foldseek/bin/foldseek
(complexa) [saber@rockylinux9 Proteina-Complexa]$
 

(complexa) [saber@rockylinux9 Proteina-Complexa]$ cp FreeBindCraft/functions/sc .venv/bin/
(complexa) [saber@rockylinux9 Proteina-Complexa]$ cp FreeBindCraft/functions/dssp .venv/bin/
(complexa) [saber@rockylinux9 Proteina-Complexa]$ chmod +x .venv/bin/deep
(complexa) [saber@rockylinux9 Proteina-Complexa]$ cp foldseek/bin/foldseek .venv/bin/
 
(complexa) [saber@rockylinux9 Proteina-Complexa]$ vi .env
UV_SC_EXEC=${LOCAL_CODE_PATH}/env/docker/internal/sc
 ↓
UV_SC_EXEC=${UV_VENV}/bin/sc
(complexa) [saber@rockylinux9 Proteina-Complexa]$

(complexa) [saber@rockylinux9 Proteina-Complexa]$ complexa init uv
(complexa) [saber@rockylinux9 Proteina-Complexa]$ source env.sh
Complexa environment initialized for uv runtime.
 
(complexa) [saber@rockylinux9 Proteina-Complexa]$ complexa design configs/search_binder_local_pipeline.yaml     ++run_name=pdl1_test     ++generation.task_name=02_PDL1