Improved structural modelling of antibodies and their complexes with clustered diffusion ensembles

The dataset contains the data used in the paper "Improved structural modelling of antibodies and their complexes with clustered diffusion ensembles". More specifically, the following files are available: colabfold.zip : list of colabfold_batch results for the 54 antibodies discussed in the manuscript alphaflow.zip : directory containing AlphaFlow ensembles for the 54 antibodies discussed in the manuscript (1000 models per PDB) colabfold_antigen.zip : directory containing the colabfold_batch results for the 17 PDBs with low H3 loop PLDDT (low-80 dataset, see manuscript). Here the sequence of the antigen is also provided. clustered_alphaflow_ensembles.zip : directory containing all the used clustered AlphaFlow ensembles for the 17 PDBs part of the LOW-80 dataset. 7*.tgz : files with all the docking runs described in the manuscript several bash script are also available. They allow one to reproduce the results obtained in the paper. In order to use them: clone the repository https://github.com/haddocking/alphaflow-antibodies/ and follow the installation instructions download all the zip and script files in the data directory of the downloaded repository (https://github.com/haddocking/alphaflow-antibodies/tree/main/data) unzip the compressed zip files execute the scripts in this order: colabfold_analysis_cmds.sh / colabfold_heavy_analysis_cmds colabfold_antigen_analysis_cmds / colabfold_antigen_heavy_analysis_cmds alphaflow_analysis_cmds alphaflow_clustered_ensemble_lines本数据集包含论文《改进型抗体及其复合物的聚类扩散集成结构建模》（Improved structural modelling of antibodies and their complexes with clustered diffusion ensembles）中使用的全部相关数据。具体可获取的文件如下： - colabfold.zip：本文稿中讨论的54种抗体的colabfold_batch运行结果列表。 - alphaflow.zip：包含本文稿中讨论的54种抗体的AlphaFlow集成结果的目录，每个蛋白质数据库（Protein Data Bank，PDB）结构对应1000个模型。 - colabfold_antigen.zip：包含17个H3环PLDDT值较低的PDB结构的colabfold_batch运行结果的目录（即LOW-80数据集，详见本文稿），该目录中同时提供了对应抗原的序列信息。 - clustered_alphaflow_ensembles.zip：包含LOW-80数据集中17个PDB结构所用的全部聚类AlphaFlow集成结果的目录。 - 7*.tgz：包含本文稿中所述全部对接运行实验结果的文件。 此外还提供了若干Bash脚本，可用于复现本文稿中得到的全部实验结果。 若要使用这些脚本，请按以下步骤操作： 1. 克隆仓库https://github.com/haddocking/alphaflow-antibodies/，并按照仓库内的安装说明完成环境配置。 2. 将所有压缩包与脚本文件下载至已克隆仓库的data目录中（仓库路径：https://github.com/haddocking/alphaflow-antibodies/tree/main/data）。 3. 解压所有压缩文件。 4. 按以下顺序执行脚本： - colabfold_analysis_cmds.sh / colabfold_heavy_analysis_cmds - colabfold_antigen_analysis_cmds / colabfold_antigen_heavy_analysis_cmds - alphaflow_analysis_cmds - alphaflow_clustered_ensemble_lines