AlphaFold3 Tutorial

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在线使用AlphaFold3

用PDB: 8BF8为例，运行AlphaFold3 Server，输入序列：

>8bf8_A
MIRNKAFVVRLYPNAAQTELINRTLGSARFVYNHFLARRIAAYLTYGQTSSELTLLKQAEETSWLSEVDK
FALQNSLKNLETAYKNFFRFPRFRKKRTGESYRTQFTNNNIQIGEGRLKLPKLGWVKTKGQQDIQGKILN
VTVRRIHEGHYEASVLCEVEIPYLPAAPKFAAGVDVGIKDFAIVTDGVRFKHEQNPKYYRSTLKRLRKAQ
QTLSRRKKGSARYGKAKTKLARIHKRIVNKRQDFLHKLTTSLVREYEIIGAGWGEFIRQLEYKAAWYGRL
VSKDRDENAALNIRREALVAAG
>8bf8_B
GUUGGUGGCUGCGGGAAUCUCAGACACCUUAAACGCUCAUGGAGGCUAUGUCAGACCUGGGCAAUGGUCU
GCGAAGUGAGAAUCACGCGACGUCGUGUGAGGUUCAAGAGU

本地部署AlphaFold3

JSON 文件示例：

{
    "dialect": "alphafold3",
    "version": 1,
    "name": "fastpet",
    "sequences": [
        {
            "protein": {
                "id": "A",
                "sequence": "TNPYARGPNPTAASLEASAGPFTVRSFTVSRPSGYGAGTVYYPTNAGGTVGAIAIVPGYTARQSSIKWWGPRLASHGFVVITIDTNSTLDQPESRSSQQMAALRQVASLNGTSSSPIYGKVDTARMGVMGWSMGGGGSLISAANNPSLKAAAPQAPWHSSTNFSSVTVPTLIFACENDSIAPVNSSALPIYDSMSQNAKQFLEIKGGSHSCANSGNSNQALIGKKGVAWMKRFMDNDTRYSTFACENPNSTAVSDFRTANC"
            }
        },
        {
            "ligand": {
                "id": "B",
                "smiles": "C1=CC(=CC=C1C(=O)O)C(=O)OCCCCOC(=O)C2=CC=C(C=C2)C(=O)OCCCCOC(=O)C3=CC=C(C=C3)C(=O)O"
            }
        }
    ],
    "modelSeeds": [
        42
    ]
}

data.json 文件示例：

{
  "dialect": "alphafold3",
  "version": 2,
  "name": "fastpet",
  "sequences": [
    {
      "protein": {
        "id": "A",
        "sequence": "TNPYARGPNPTAASLEASAGPFTVRSFTVSRPSGYGAGTVYYPTNAGGTVGAIAIVPGYTARQSSIKWWGPRLASHGFVVITIDTNSTLDQPESRSSQQMAALRQVASLNGTSSSPIYGKVDTARMGVMGWSMGGGGSLISAANNPSLKAAAPQAPWHSSTNFSSVTVPTLIFACENDSIAPVNSSALPIYDSMSQNAKQFLEIKGGSHSCANSGNSNQALIGKKGVAWMKRFMDNDTRYSTFACENPNSTAVSDFRTANC",
        "modifications": [],
        "unpairedMsa": ""
        "pairedMsa": ""
        "templates": []
      }
    },
    {
      "ligand": {
        "id": "B",
        "smiles": "C1=CC(=CC=C1C(=O)O)C(=O)OCCCCOC(=O)C2=CC=C(C=C2)C(=O)OCCCCOC(=O)C3=CC=C(C=C3)C(=O)O"
      }
    }
  ],
  "modelSeeds": [
    42
  ],
  "bondedAtomPairs": null,
  "userCCD": null
}

蛋白功能注释

重要工具：FoldSeek

从UniProt开始注释功能：