ECOD 2027 版重建网页界面并更新蛋白结构域分类
ECOD in 2027: a modernized interface and an updated classification of protein domains
进化分类数据库 ECOD 发布 2027 版，完成网页资源整体重建，并更新蛋白结构域分类。ECOD 目前收录 290 万个结构域，其中约 137 万个来自 PDB 实验结构，151 万个来自 AlphaFold 蛋白结构数据库的预测模型。检索改为序列、结构、关键词三种方式，Foldseek 成为网页端主要检索方法，检索对象为约 45.7 万个代表性结构域数据库，该库也对外分发供本地使用；结果通过 Mol* 交互查看器展示，并新增 API 供程序化访问。
来源：Nucleic Acids Research · doi.org
数据库重建后把 Foldseek 设为默认检索并开放 API，做蛋白结构注释的读者可据此调整查询与批量接入方式。
The Evolutionary Classification of Domains (ECOD) organizes protein domains into a hierarchy of evolutionary relationships, encompassing both experimentally determined and computationally predicted structures. ECOD now classifies 2.9M domains, of which ∼1.37M derived from the Protein Data Bank and 1.51M from predicted models in the AlphaFold Protein Structure Database. The principal development we report here is a complete rebuild of the ECOD web resource. Search has been reconstructed around three modalities: (i) sequence, (ii) structure, and (iii) keyword. Foldseek now is the primary search method for the ECOD web page, searching a ∼457k representative domain database that is also distributed for local use. Results are presented through a Mol* interactive viewer, and a new API has been developed for programmatic access to the database. Alongside the interface, the pipeline for classifying new PDB entries has been rebuilt and returned to a regular cadence, family groups have been synchronized with Pfam v38.2, the bulk distributables have been reorganized and now include the search databases, the ligands in contact with each domain are recorded for experimental structures and annotated with drug cross-references from DrugDomain, and a registry has been introduced through which ECOD assigns stable identifiers to gene-called proteins and records the structures it predicts. ECOD is freely available at http://prodata.swmed.edu/ecod.