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Bio Proteinmpnn Inference

skill-onescience-ai-oneskills-proteinmpnn-inference · by onescience-ai

ProteinMPNN inverse folding 推理 skill。用于执行 OneScience ProteinMPNN 的 PDB 骨架到序列设计、score-only、conditional probabilities、fixed chains、fixed positions、tied positions、PSSM、omit AA 和 CA-only 推理，收紧 JSONL helper、chain_M、权重目录、采样温度和 FASTA/score 输出校验。

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Install

$ agentstack add skill-onescience-ai-oneskills-proteinmpnn-inference

✓ scanned · ✓ verified — works with Claude Code, Cursor, and more.

Security review

✓ Passed

No issues found. Passed automated security review. · v0.1.0 How review works →

  • ✓ Prompt-injection patterns
  • ✓ Secret / credential exfiltration
  • ✓ Dangerous shell & filesystem operations
  • ✓ Untrusted network calls
  • ✓ Known-malicious package signatures

What it can access

  • ✓ Network access No
  • ✓ Filesystem access No
  • ✓ Shell / process execution No
  • ✓ Environment & secrets No
  • ✓ Dynamic code execution No

From automated source analysis of v0.1.0. “Used” means the capability is present in the source — more access means more to trust, not that it’s unsafe.

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About

ProteinMPNN 推理

使用边界

用于给已有骨架设计或打分序列。它不是结构预测模型。若上游骨架来自 RFdiffusion，先确认 PDB/链/残基编号，再进入本 skill。

可复用资源

  • {onescience_path}/onescience/examples/biosciences/_manifests/model_requests/proteinmpnn_request.yaml：PDB、链、固定位置、采样温度、权重和输出模板。
  • references/proteinmpnn_execution.md：helper JSON、CA-only、score-only 和约束检查。

推荐流程

  1. 读模型卡：onescience-coder/assets/models/proteinmpnn.md。
  2. 固定入口：{onescience_path}/onescience/examples/biosciences/ProteinMPNN/protein_mpnn_run.py。
  3. Preflight：PDB backbone 是否含 N/CA/C/O，链 ID，设计链，固定位置，权重目录和模型名。
  4. 如果有复杂约束，先生成 helper JSON：chain id、fixed positions、tied positions、PSSM、omit AA。
  5. 运行：设置 --sampling_temp、--num_seq_per_target、--batch_size、--seed。
  6. Postflight：FASTA 数量、score/probs、固定位置是否保持、设计链是否正确。

禁止事项

  • 不要把 chain_M 与 padding mask 混用。
  • CA-only 权重必须配套 --ca_only 和 CA-only 输入。
  • 不要在 PDB 原子缺失或链名不明时直接设计。

Source & license

This open-source skill is cataloged on AgentStack and links to its original source — we do not rehost the code.

Install and usage instructions live in the source repository linked above.

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Versions

  • v0.1.0 Imported from the upstream source.

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