免费在 GitHub 公开

query-pdb

Query RCSB PDB for experimental protein structures. Use when user asks about crystal structures, X-ray, cryo-EM, NMR structures, or PDB IDs. Triggers on "pdb", "crystal structure", "cryo-em", "x-ray structure", "protein crystal", "experimental structure".

中文简介正在准备中。当前显示原文说明。

BioTender-max/awesome-bio-agent-skills

查看安装方法

包含的文件（1）

SKILL.md3.6 KB

SKILL.md（原文）

安装前可以查看交给 AI 代理的指令内容。

RCSB PDB Database Query

Query the RCSB Protein Data Bank for experimental 3D structures.

When to Use

User asks for experimental structures of a protein
User provides a PDB ID (e.g., "6LU7")
User wants to find structures solved by X-ray, cryo-EM, or NMR
User asks about resolution, ligands, or binding sites

How to Execute

import requests
import json

# 1. Text search (simple keyword)
def search_pdb(query_text, max_results=5):
    url = "https://search.rcsb.org/rcsbsearch/v2/query"
    query = {
        "query": {
            "type": "terminal",
            "service": "full_text",
            "parameters": {"value": query_text}
        },
        "return_type": "entry",
        "request_options": {"paginate": {"start": 0, "rows": max_results}}
    }
    r = requests.post(url, json=query)
    r.raise_for_status()
    return r.json()

# 2. Advanced search (by gene + organism + method)
def advanced_search_pdb(gene_name, organism="Homo sapiens", method=None, max_results=5):
    nodes = [
        {"type": "terminal", "service": "text",
         "parameters": {"attribute": "rcsb_entity_source_organism.rcsb_gene_name.value",
                        "operator": "exact_match", "value": gene_name}},
        {"type": "terminal", "service": "text",
         "parameters": {"attribute": "rcsb_entity_source_organism.ncbi_scientific_name",
                        "operator": "exact_match", "value": organism}}
    ]
    if method:
        nodes.append({"type": "terminal", "service": "text",
                      "parameters": {"attribute": "exptl.method", "operator": "exact_match", "value": method}})
    query = {
        "query": {"type": "group", "logical_operator": "and", "nodes": nodes},
        "return_type": "entry",
        "request_options": {"paginate": {"start": 0, "rows": max_results},
                           "sort": [{"sort_by": "rcsb_accession_info.deposit_date", "direction": "desc"}]}
    }
    r = requests.post("https://search.rcsb.org/rcsbsearch/v2/query", json=query)
    r.raise_for_status()
    return r.json()

# 3. Get entry details
def get_pdb_entry(pdb_id):
    url = f"https://data.rcsb.org/rest/v1/core/entry/{pdb_id}"
    r = requests.get(url)
    r.raise_for_status()
    return r.json()

# 4. Download structure
def download_pdb(pdb_id, output_dir="/workspace/group"):
    url = f"https://files.rcsb.org/download/{pdb_id}.pdb"
    r = requests.get(url)
    r.raise_for_status()
    path = f"{output_dir}/{pdb_id}.pdb"
    with open(path, 'w') as f:
        f.write(r.text)
    return path

# Example
results = search_pdb("human insulin")
for hit in results.get("result_set", []):
    pdb_id = hit["identifier"]
    details = get_pdb_entry(pdb_id)
    title = details.get("struct", {}).get("title", "N/A")
    method = details.get("exptl", [{}])[0].get("method", "N/A")
    resolution = details.get("rcsb_entry_info", {}).get("resolution_combined", ["N/A"])[0]
    print(f"{pdb_id}: {title}")
    print(f"  Method: {method}, Resolution: {resolution} Å")

Common Methods

X-RAY DIFFRACTION — crystal structures
ELECTRON MICROSCOPY — cryo-EM
SOLUTION NMR — NMR in solution

Follow-up Suggestions

"Want me to download this structure and analyze binding sites?"
"Should I compare with the AlphaFold prediction?"
"Want me to find ligands bound in this structure?"

评价

还没有评价。欢迎分享你的使用感受。

无需登录即可发表。欢迎分享使用感受、提问，或说明在哪些环境下无法运行。

还没有评论。来写第一条吧。

同一仓库的技能

alignment-and-mapping

免费

Workflow for read alignment, sorting, indexing, mapping statistics, and downstream-ready alignment artifacts.

中文简介正在准备中。当前显示原文说明。