Soy3D Atlas - API Documentation

Overview

Soy3D Atlas API provides programmatic access to predicted protein structures and annotations. The API is organized into two main categories:

Public API: General-purpose APIs for accessing predicted structures and basic metadata.
Annotations API: APIs for accessing functional annotations and additional metadata about predicted structures.

All API responses are in JSON format by default, unless otherwise specified. The API is free to use for both academic and commercial purposes, but please refer to our licensing terms for more information.

Authentication

The Soy3D Atlas does not require authentication for most endpoints. However, there are rate limits in place to ensure fair usage of the service. For high-throughput applications, please contact us to request an API key.

To use an API key, include it in your requests using the X-API-Key header:

curl -X GET "https://ai4seed.cn/seed-api/open/getPlddt/YZW0000000002" -H "X-API-Key: your_api_key_here"

API Endpoints

Public API

General-purpose APIs for accessing predicted protein structures and metadata.

GET/open/getEntry/{accession}

Annotations API

APIs for accessing functional annotations and additional metadata about predicted structures.

GET/open/getPlddt/{accession}

Usage Examples

Python Example: Get Structure and Metadata

Retrieve protein structure metadata using accession number:

import requests

accession = "YZW0000000001"
url = f"https://ai4seed.cn/seed-api/open/getEntry/{accession}"

response = requests.get(url)

if response.status_code == 200:
    data = response.json()
    if data['code'] == 200:
        structure_info = data['data']
        print(f"Accession: {structure_info['accession']}")
        print(f"Protein ID: {structure_info['proteinId']}")
        print(f"Entity Name: {structure_info['entityName']}")
        print(f"Gene ID: {structure_info['geneId']}")
        print(f"Species: {structure_info['sapiensId']}")
        # 更多信息可以从structure_info中获取
    else:
        print(f"API Error: {data['msg']}")
else:
    print(f"HTTP Error: {response.status_code}")

Python Example: Get PLDDT Confidence Scores

Retrieve structural confidence scores for a specific accession:

import requests

accession = "YZW0000000001"
url = f"https://ai4seed.cn/seed-api/open/getPlddt/{accession}"

response = requests.get(url)

if response.status_code == 200:
    data = response.json()
    if data['code'] == 200:
        confidence_data = data['data']
        print(f"Accession: {accession}")
        print(f"pTM Score: {confidence_data['ptm']}")
        print(f"Complex pLDDT Score: {confidence_data['complex_plddt']}")
        print(f"Confidence Score: {confidence_data['confidence_score']}")
        # 可以访问更多的置信度指标
    else:
        print(f"API Error: {data['msg']}")
else:
    print(f"HTTP Error: {response.status_code}")

Rate Limits

The Soy3D Atlas is rate limited to ensure fair usage for all users. The current rate limits are:

100 requests per minute per IP address for unauthenticated requests
1,000 requests per minute per API key for authenticated requests
For bulk downloads, please use our precomputed datasets

If you need higher limits for your research or application, please contact us atyangfan@yzwlab.cn.