Protein Common Assembly Database

Protein Common Assembly Database (ProtCAD) is a comprehensive database of protein assemblies in PDB. ProtCAD contains clusters of assemblies of homologous proteins observed in multiple independent experiments, such as unique crystal forms and individual EM and NMR experiments. The term "Crystal forms" refers to independent experiments that provide evidence in favor of the structure of biological assemblies. Unique viable assemblies are built and identified that constitute the entire crystal using EPPIC and mmCIF file from PDB, removing any with disconnected chains, and adding PDB biological assemblies that are not in EPPIC.

蛋白质通用组装数据库（Protein Common Assembly Database，简称ProtCAD）是一款收录蛋白质数据银行（Protein Data Bank，PDB）内蛋白质组装体的综合性数据库。该数据库收录了多项独立实验中观测到的同源蛋白质组装簇，涵盖独特晶型以及单独的电子显微镜（Electron Microscopy，EM）与核磁共振（Nuclear Magnetic Resonance，NMR）实验结果。“晶型”这一术语指的是为生物组装体结构提供佐证依据的独立实验。研究人员借助PDB提供的EPPIC（Evolutionary Protein-Protein Interface Classifier）工具与mmCIF（macromolecular Crystallographic Information File）格式文件，构建并识别出可构成完整晶体的独特可行组装体；在此过程中剔除存在断裂链的组装体，并补充未被EPPIC收录的PDB生物组装体。

搜集汇总

背景与挑战

背景概述

Protein Common Assembly Database（ProtCAD）是一个综合性的蛋白质组装数据库，基于PDB中的同源蛋白在多个独立实验中的观察结果进行聚类。它通过EPPIC和mmCIF文件构建唯一可行的组装，并基于化学计量学、对称性和界面共享性进行聚类分析。该数据库为蛋白质复合物结构预测提供了基准测试和训练数据集，尤其在深度学习结构预测领域具有应用价值。