Metalloprotein AlphaFold set with enzyme/non-enzyme labeled sites

<pre>The AlphaFold set contains computationally generated structures for metalloproteins that were used to test MAHOMES II's enzyme/non-enzyme predictive performance (Feehan et al. 2023). README.md - Detailed description of AlphaFold set generation. AF-...-model_v2.pdb - Files with the 3D atomic coordinates of a metalloprotein. MAHOMES-II_AlphaFold_set_site_data.csv - Contains the data used during the generation of the AlphaFold set for the final sites. Columns are - Entry: The UniProt accession number of the protein with the bound metal site. - struc_id: The structures AlphaFold DB name (Febuary 2022) and the name of the file in this directory with added metal site. - metal_resName: The two letter PDB residue abbreviation for the site's metal - metal_seqID: The residue index number for the added metal ion. - Enzyme: The enzyme (True) or non-enzyme (False) label. - Entry name: UniProt entry name. - Protein names: The UniProt provided metalloprotein name(s). - Number of homologs with solved structures (PDB): Number of protein sequences in the PDB (May 21, 2020) with an E-value &lt; 1. - Number of homologs in MAHOMES II dataset and T-metal-sites10: Number of protein sequences used to train and evaluate MAHOMES II with an E-value &lt; 1 (0 for all entries). - Metal binding note: UniProt metal binding note that includes information covering the metal’s identity and catalytic flag. - Metal coordinating residue seqIDs: The sequence indices for the metal coordinating residues included in the UniProt’s metal binding section.</pre>本AlphaFold数据集包含用于测试MAHOMES II酶/非酶预测性能的金属蛋白质计算生成结构（Feehan等，2023）。 README.md：详细说明AlphaFold数据集的生成流程。 AF-...-model_v2.pdb：存储金属蛋白质三维原子坐标的文件。 MAHOMES-II_AlphaFold_set_site_data.csv：包含本AlphaFold数据集最终位点生成过程中所用的全部相关数据，各字段说明如下： - Entry：绑定金属位点的蛋白质的通用蛋白质知识库（UniProt）登录号 - struc_id：AlphaFold数据库的结构名称（2022年2月版）以及本目录下添加了金属位点的文件名 - metal_resName：该位点金属的PDB残基双字母缩写 - metal_seqID：所添加金属离子的残基索引编号 - Enzyme：酶（True）或非酶（False）标签 - Entry name：UniProt条目名称 - Protein names：通用蛋白质知识库提供的金属蛋白质名称 - Number of homologs with solved structures (PDB)：蛋白质数据库（PDB）中E值<1的已解析结构同源蛋白序列数量（统计截止日期：2020年5月21日） - Number of homologs in MAHOMES II dataset and T-metal-sites10：在MAHOMES II数据集中用于训练与评估模型且E值<1的蛋白序列数量（所有条目均为0） - Metal binding note：通用蛋白质知识库提供的金属结合注释，涵盖金属种类及催化标记相关信息 - Metal coordinating residue seqIDs：通用蛋白质知识库金属结合部分中收录的金属配位残基的序列索引