mTM-align2: A Server for Real-time Protein Structure Database Search and Alignment

Identifying structurally similar proteins from large-scale databases is a fundamental challenge in structural bioinformatics. The recent release of millions of predicted structures by AlphaFold2 presents unprecedented scale and efficiency challenges for existing tools. To address this, we introduce the mTM-align2 server, a significantly upgraded version of mTM-align. This new platform is capable of searching both monomeric and multimeric structures against a comprehensive database of approximately 3 million entries in seconds. mTM-align2 achieves a two- to three-fold increase in search speed while maintaining accuracy comparable to that of other state-of-the-art methods. The server is available at https://yanglab.qd.sdu.edu.cn/mTM-align/.