DBAASP v4 发布：抗菌肽数据库扩展到条件分辨的活性与化学结构
DBAASP V4: condition-resolved bioactivity and chemical structures for data-driven peptide and peptidomimetic discovery
抗菌肽活性与结构数据库 DBAASP 发布 v4，条目超过 25 000 条，并从以序列为中心扩展为结构感知的资源库。新版系统加入 SMILES 表示、链内键与环结构的注释、专门的抗生物膜与协同作用记录、PubChem 链接、超过 9200 条分子动力学轨迹以及新的预测服务。数据库由人工整理，把肽和拟肽与定量的抗菌、抗生物膜、抗癌、溶血和哺乳动物细胞毒性测量及其实验条件关联起来。作者指出，这类条件分辨的数据可用于监督学习、菌株与靶点特异模型、模型校准以及遗传算法的替代适合度函数，SMILES 表示还能支持难以仅用序列描述的非天然肽和拟肽建模。
来源：Nucleic Acids Research · doi.org
数据库把抗菌肽活性数据与实验条件、SMILES 结构和动力学轨迹绑定，为肽与拟肽的监督学习提供可校准标签。
The current peptide renaissance—driven by metagenomic and proteomic mining, molecular de-extinction, protein language models, and generative or evolutionary design—is producing millions of candidates, but useful machine learning depends on experimentally anchored, context-rich labels. The Database of Antimicrobial Activity and Structure of Peptides (DBAASP) is a manually curated resource linking peptides and peptidomimetics to quantitative antimicrobial, antibiofilm, anticancer, hemolytic, and mammalian-cell cytotoxicity measurements and their experimental conditions. DBAASP v4 contains >25 000 entries and extends the resource from a sequence-centered database to a structure-aware repository. Major additions include systematic SMILES representations, enhanced annotation of intrachain bonds and ring architectures, dedicated antibiofilm, and synergy records, PubChem links, >9200 molecular-dynamics trajectories, and new prediction services. The condition-resolved data support supervised learning, strain-, and target-specific models, model calibration, and surrogate fitness functions for genetic algorithms. SMILES representations further enable modeling of noncanonical peptides and peptidomimetics that cannot be adequately described by sequence alone. DBAASP therefore complements large peptide catalogues by providing the experimentally curated activity and structure layers, needed to convert sequence information into testable predictions, design, and optimization of biologically active compounds. DBAASP v4 is freely available at https://dbaasp.org.