proteinmpnn-nim

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🇺🇸

Original

English

🇨🇳

Translation

Chinese

ProteinMPNN NIM

Design protein sequences for a supplied backbone PDB. Use this

SKILL.md

for first-pass hosted/local usage; load supplemental files only when needed:

```
references/api.md
```
: exact endpoints, schemas, Docker flags, response fields.
```
references/science.md
```
: inverse-folding uses, limits, and validation.
```
references/parameters.md
```
: design controls, fixed positions, sampling.
```
references/validation.md
```
: FASTA, score, and structure checks.
```
references/examples.md
```
: compact hosted/local request patterns.

为提供的骨架PDB设计蛋白质序列。使用本

SKILL.md

进行首次托管/本地部署使用；仅在需要时加载补充文件：

```
references/api.md
```
：精确的端点、模式、Docker参数、响应字段。
```
references/science.md
```
：反向折叠的用途、限制与验证方法。
```
references/parameters.md
```
：设计控制、固定位置、采样设置。
```
references/validation.md
```
：FASTA、评分与结构检查规则。
```
references/examples.md
```
：简洁的托管/本地请求示例。

Choose Mode

选择运行模式

Honor an explicitly configured runtime before asking.

NIM_API_MODE=local

selects the local service at

PROTEINMPNN_NIM_URL

; the URL defaults to

http://localhost:8000

for a NIM running in the same host or container. Ask only when neither the environment nor the user's request makes the mode clear:

Hosted NVIDIA API or local Docker NIM?

Hosted:

https://health.api.nvidia.com/v1/biology/ipd/proteinmpnn/predict

Local:

${PROTEINMPNN_NIM_URL:-http://localhost:8000}/biology/ipd/proteinmpnn/predict

Local inference paths do not include

/v1/

. Hosted requests use

Authorization: Bearer $NGC_API_KEY

. Supported local Docker startup uses

NGC_API_KEY

(or

NVIDIA_API_KEY

via the preflight) for registry login, entitlement checks, and first-run model downloads; pass it into the container with

-e NGC_API_KEY

. Local inference requests use no auth header after readiness. Warm-cache key-free startup varies by image/version and should not be assumed.

优先使用明确配置的运行时环境，若未明确则询问用户。设置

NIM_API_MODE=local

将选择

PROTEINMPNN_NIM_URL

指向的本地服务；若未指定该URL，默认使用同一主机或容器中运行的NIM地址

http://localhost:8000

。仅当环境配置和用户请求均未明确运行模式时，才询问用户：

使用托管式NVIDIA API还是本地Docker NIM？

托管式：

https://health.api.nvidia.com/v1/biology/ipd/proteinmpnn/predict

本地：

${PROTEINMPNN_NIM_URL:-http://localhost:8000}/biology/ipd/proteinmpnn/predict

本地推理路径不包含

/v1/

。托管式请求需使用

Authorization: Bearer $NGC_API_KEY

头信息。本地Docker启动时，需使用

NGC_API_KEY

（或通过预检查使用

NVIDIA_API_KEY

）进行镜像仓库登录、权限验证和首次模型下载；通过

-e NGC_API_KEY

将其传入容器。本地推理服务就绪后，请求无需携带认证头。无密钥的预热缓存启动方式因镜像版本而异，请勿默认依赖该方式。

Local Docker

本地Docker部署

For local setup, run the full sequence — env preflight,

docker login

docker run

, readiness loop, then the no-auth localhost request; do not answer with only a localhost Python request. For the exact preflight (

.env

sourcing,

NGC_API_KEY

NVIDIA_API_KEY

handling, and the

docker run

for

nvcr.io/nim/ipd/proteinmpnn:latest

), copy the command block in

references/api.md

under Docker Reference verbatim. This NIM's cache mount is

/home/nvs/.cache/nim

, not

/opt/nim/.cache

. When

PROTEINMPNN_NIM_URL

is supplied, the service is already managed elsewhere; use that URL and do not start another Docker container.

Readiness:

bash

proteinmpnn_nim_url="${PROTEINMPNN_NIM_URL:-http://localhost:8000}"
until curl -sf "${proteinmpnn_nim_url%/}/v1/health/ready"; do sleep 5; done

本地部署需执行完整流程——环境预检查、

docker login

、

docker run

、就绪状态轮询，然后发起无认证的本地请求；请勿仅返回本地Python请求代码。关于精确的预检查步骤（

.env

文件加载、

NGC_API_KEY

NVIDIA_API_KEY

处理，以及

nvcr.io/nim/ipd/proteinmpnn:latest

的

docker run

命令），请直接复制

references/api.md

中Docker参考下的命令块。本NIM的缓存挂载路径为

/home/nvs/.cache/nim

，而非

/opt/nim/.cache

。若已提供

PROTEINMPNN_NIM_URL

，说明服务已在其他位置管理；直接使用该URL，无需启动新的Docker容器。

就绪状态检查：

bash

proteinmpnn_nim_url="${PROTEINMPNN_NIM_URL:-http://localhost:8000}"
until curl -sf "${proteinmpnn_nim_url%/}/v1/health/ready"; do sleep 5; done

Request Pattern

请求模式

Read PDB content inline; do not send only a file path.

python

import os
from pathlib import Path
import requests

HOSTED = os.getenv("NIM_API_MODE", "hosted").strip().lower() != "local"
pdb_content = Path("1R42.pdb").read_text()
nim_url = os.getenv("PROTEINMPNN_NIM_URL", "http://localhost:8000").rstrip("/")
url = (
    "https://health.api.nvidia.com/v1/biology/ipd/proteinmpnn/predict"
    if HOSTED else f"{nim_url}/biology/ipd/proteinmpnn/predict"
)
headers = {"Content-Type": "application/json"}
if HOSTED:
    headers["Authorization"] = f"Bearer {os.environ['NGC_API_KEY']}"

payload = {
    "input_pdb": pdb_content,
    "num_seq_per_target": 10,
    "sampling_temp": [0.1],
    "use_soluble_model": False,
    "ca_only": False,
}
response = requests.post(url, headers=headers, json=payload, timeout=300)
response.raise_for_status()
result = response.json()

Common controls:

Redesign only chain A:
```
"input_pdb_chains": ["A"]
```
.
Exclude amino acids:
```
"omit_AAs": ["C"]
```
or
```
"omit_AAs": ["M"]
```
.
Diversity:
```
"sampling_temp": [0.1, 0.3, 0.5]
```
(always a list).
Solubility bias:
```
"use_soluble_model": True
```
.
Candidate count:
```
num_seq_per_target
```
is 1-100.

直接读取PDB内容嵌入请求；请勿仅发送文件路径。

python

import os
from pathlib import Path
import requests

HOSTED = os.getenv("NIM_API_MODE", "hosted").strip().lower() != "local"
pdb_content = Path("1R42.pdb").read_text()
nim_url = os.getenv("PROTEINMPNN_NIM_URL", "http://localhost:8000").rstrip("/")
url = (
    "https://health.api.nvidia.com/v1/biology/ipd/proteinmpnn/predict"
    if HOSTED else f"{nim_url}/biology/ipd/proteinmpnn/predict"
)
headers = {"Content-Type": "application/json"}
if HOSTED:
    headers["Authorization"] = f"Bearer {os.environ['NGC_API_KEY']}"

payload = {
    "input_pdb": pdb_content,
    "num_seq_per_target": 10,
    "sampling_temp": [0.1],
    "use_soluble_model": False,
    "ca_only": False,
}
response = requests.post(url, headers=headers, json=payload, timeout=300)
response.raise_for_status()
result = response.json()

常用控制参数：

仅重设计A链：
```
"input_pdb_chains": ["A"]
```
。
排除特定氨基酸：
```
"omit_AAs": ["C"]
```
或
```
"omit_AAs": ["M"]
```
。
多样性设置：
```
"sampling_temp": [0.1, 0.3, 0.5]
```
（必须为列表格式）。
可溶性偏好：
```
"use_soluble_model": True
```
。
候选序列数量：
```
num_seq_per_target
```
取值范围为1-100。

Save And Report Output

保存并报告输出结果

Save the returned

mfasta

and pair scores only with designed (non-native/WT) rows, using the snippet in

references/examples.md

under Save Multi-FASTA. Validate promising designs by predicting structures with Boltz2 or OpenFold3 and comparing them to the target backbone. For FASTA/score sanity checks, read

references/validation.md

保存返回的

mfasta

文件，并仅将评分与设计的（非天然/野生型）序列行配对，可使用

references/examples.md

中保存多FASTA下的代码片段。通过Boltz2或OpenFold3预测候选设计的结构，并与目标骨架对比，以此验证设计的可行性。关于FASTA/评分的合理性检查，请参考

references/validation.md

。

Limits And Troubleshooting

限制与故障排查

Minimum GPU VRAM: about 3 GB.
```
sampling_temp
```
must be a list, even for one value.
Empty
```
mfasta
```
: check non-empty
```
input_pdb
```
and
```
num_seq_per_target >= 1
```
.
PDB parse errors: use valid PDB ATOM records.
Local URL 404 usually means an accidental
```
/v1/
```
prefix.
Cache mount error: use
```
/home/nvs/.cache/nim
```
inside the container.

最低GPU显存要求：约3GB。
```
sampling_temp
```
必须为列表格式，即使仅设置一个值。
```
mfasta
```
为空：检查
```
input_pdb
```
是否非空，且
```
num_seq_per_target >= 1
```
。
PDB解析错误：确保使用有效的PDB ATOM记录。
本地URL返回404：通常是意外添加了
```
/v1/
```
前缀。
缓存挂载错误：容器内使用
```
/home/nvs/.cache/nim
```
路径。