PLMSearch: Protein language model powers accurate and fast sequence search for remote homology.

ABSTRACT: Homologous protein search is one of the most commonly used methods for protein annotation and analysis. Compared to structure search, detecting distant evolutionary relationships from sequences alone remains challenging. Here we propose PLMSearch (Protein Language Model), a homologous protein search method with only sequences as input. PLMSearch uses deep representations from a pre-trained protein language model and trains the similarity prediction model with a large number of real structure similarity. This enables PLMSearch to capture the remote homology information concealed behind the sequences. Extensive experimental results show that PLMSearch can search millions of query-target protein pairs in seconds like MMseqs2 while increasing the sensitivity by more than threefold, and is comp

SUBMITTER: Liu W 

PROVIDER: S-EPMC10981738 | biostudies-literature | 2024 Mar

REPOSITORIES: biostudies-literature