PSP - 蛋白质复合物结构预测 Template 的 Multichain Mask 2D (二维多链掩码)

news2024/11/17 8:27:58

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在蛋白质复合物结构预测中，AlphaFold2 Multimer 的 Multichain Mask 2D 对于模版特征 (Template) 的影响较大，默认使用单链进行模版搜索，关闭链间 Docking 信息，只保留链内信息，当单链来源自同一个模版时，则可以保留链间信息。

测试 Case，8BBY：

>A
MSKVETGDQGYTVVQSKYKKAVEQLQKGLLDGEIKIFFEGTLASTIYCLHKVDNKLDNLGDGDYVDFLIITKLRILNAKEETIDIDASSSKTAQDLAKKYVFNKTDLNTLYRVLNGDEADTNRLVEEVSGKYQVVLYPEGKRV
>B
AAKASIADENSPVKLTLKSDKKKDLKDYVDDLRTYNNGYSNAIEVAGEDRIETAIALSQKYYNSDDENAIFRDSVDNVVLVGGNAIVDGLVASPLASEKKAPLLLTSKDKLDSSVKAEIKRVMNIKSTTGINTSKKVYLAGGVNSISKEVENELKDMGLKVTRLAGDDRYETSLKIADEVGLDNDKAFVVGGTGLADAMSIAPVASQLRNANGKMDLADGDATPIVVVDGKAKTINDDVKDFLDDSQVDIIGGENSVSKDVENAIDDATGKSPDRYSGDDRQATNAKVIKESSYYQDNLNNDKKVVNFFVAKDGSTKEDQLVDALAAAPVAANFGVTLNSDGKPVDKDGKVLTGSDNDKNKLVSPAPIVLATDSLSSDQSVSISKVLDKDNGENLVQVGKGIATSVINKLKDLLSM
>C
DMSKVETGDQGYTVVQSKYKKAVEQIKIFFEGTLAYCLHKVDNKLDNLGDGDYVDFLIITKLRILNAKEETIDIDASSSKTAQDLAKKYVFNKTDLNTLYRVLNGDEADTNRVEEVSGKYQVVLYPEGKRV
>D
ASIADENSPVKLTLKSDKKKDLKDYVDDLRTYNNGYSNAIEVAGEDRIETAIALSQKYYNSDDENAIFRDSVDNVVLVGGNAIVDGLVASPLASEKKAPLLLTSKDKLDSSVKAEIKRVMNIKSTTGINTSKKVYLAGGVNSISKEVENELKDMGLKVTRLAGDDRYETSLKIADEVGLDNDKAFVVGGTGLADAMSIAPVASQLRNANGKMDLADGDATPIVVVDGKAKTINDDVKDFLDDSQVDIIGGENSVSKDVENAIDDATGKSPDRYSGDDRQATNAKVIKESSYYQDNLNNDKKVVNFFVAKDGSTKEDQLVDALAAAPVAANFGVTLNSDGKPVDKDGKVLTGSDNDKNKLVSPAPIVLATDSLSSDQSVSISKVLDKDNGENLVQVGKGIATSVINKLKDLLS

使用单链 GT PDB 作为 Template 时，TMScore 是 0.4954，增加链间的 Docking 信息，TMScore 提升至 0.9917，提升很大。

预测结构 (0.9917) 蓝色与真实结构的比较如下：

逻辑位于 openfold/model/model.py，增加 globals.use_template_unmask 参数，修改逻辑：

if not self.globals.use_template_unmask:
    multichain_mask_2d = (asym_id[..., None] == asym_id[..., None, :])  # [N_res, N_res]
else:
    # 保留链内信息
    # mask_inter = (asym_id[..., None] == asym_id[..., None, :])
    # 保留链间信息
    # mask_intra = (asym_id[..., None] != asym_id[..., None, :])  # [N_res, N_res]
    # 保留全部信息
    tmp_tensor = torch.ones(asym_id.shape, dtype=asym_id.dtype).to(asym_id.device)
    mask_none = (tmp_tensor[..., None] == tmp_tensor[..., None, :])
    mask_list = []
    for i in range(n_tmpl):
        # if i == 0:
        #     mask_list.append(mask_inter)
        # else:
        #     mask_list.append(mask_intra)
        mask_list.append(mask_none)
    multichain_mask_2d = torch.stack(mask_list, dim=0)
    logger.info(f"[CL] use_template_unmask: {self.globals.use_template_unmask}, "
                f"multichain_mask_2d: {multichain_mask_2d.shape}")

# -------------- 验证 multichain_mask_2d -------------- #
# tmp = multichain_mask_2d.cpu().numpy()
# import pickle
# with open("multichain_mask_2d.pkl", "wb") as f:
#     pickle.dump(tmp, f)
# logger.info(f"[CL] saved multichain_mask_2d!")
# -------------- 验证 multichain_mask_2d -------------- #

# 调用逻辑
template_embeds = self.template_embedder(
    template_feats,
    z,
    pair_mask.to(dtype=z.dtype),
    no_batch_dims,
    chunk_size=self.globals.chunk_size,
    multichain_mask_2d=multichain_mask_2d,
    use_fa=self.globals.use_fa,
)

只保留链内信息：

multichain_mask_2d = (asym_id[..., None] == asym_id[..., None, :])  # [N_res, N_res]

只保留链间信息：

# 保留链间信息
multichain_mask_2d = (asym_id[..., None] != asym_id[..., None, :])  # [N_res, N_res]

保留全部(链内和链间)信息：

tmp_tensor = torch.ones(asym_id.shape, dtype=asym_id.dtype).to(asym_id.device)
multichain_mask_2d = (tmp_tensor[..., None] == tmp_tensor[..., None, :])

其中 multichain_mask_2d 特征，4 个特征，2 个链内 Mask，2 个链间 Mask，即：

Mask

其中，template_feats 特征维度，如下：

template_feats, template_all_atom_positions: torch.Size([4, 1102, 37, 3])
template_feats, template_all_atom_mask: torch.Size([4, 1102, 37])
template_feats, template_aatype: torch.Size([4, 1102])
template_feats, template_mask: torch.Size([4])
template_feats, template_pseudo_beta: torch.Size([4, 1102, 3])
template_feats, template_pseudo_beta_mask: torch.Size([4, 1102])
template_feats, template_torsion_angles_sin_cos: torch.Size([4, 1102, 7, 2])
template_feats, template_alt_torsion_angles_sin_cos: torch.Size([4, 1102, 7, 2])
template_feats, template_torsion_angles_mask: torch.Size([4, 1102, 7])

具体逻辑位于 openfold/model/embedders.py#TemplateEmbedderMultimer，即：

其中，循环处理多个 Template

for i in range(n_templ):
    pair_act = self.template_pair_embedder(
        template_dgram,
        aatype_one_hot,
        z,
        pseudo_beta_mask,
        backbone_mask,
        multichain_mask_2d,
        unit_vector,
    )

调用 openfold/model/embedders.py#TemplatePairEmbedderMultimer，即：

# template_dgram 部分
pseudo_beta_mask_2d = pseudo_beta_mask_2d * multichain_mask_2d
template_dgram = template_dgram * pseudo_beta_mask_2d[..., None]
# ...
# rigid Rt 部分
backbone_mask_2d = backbone_mask_2d * multichain_mask_2d
x, y, z = [coord * backbone_mask_2d for coord in unit_vector]
# ...

使用 pickle 存储 Template 特征，即：

# 写入
if key == "template_all_atom_positions":
    tmp = template_feats[key].cpu().numpy()
    import pickle
    with open("template_all_atom_positions.pkl", "wb") as f:
        pickle.dump(tmp, f)
    logger.info(f"[CL] saved template_all_atom_positions!")

# 读取
def load_tensor_pkl(input_path):
    import pickle
    with open(input_path, "rb") as f:
        obj = pickle.load(f)
    # print(f"[Info] feat_dict: {obj.keys()}")
    return obj