foldseek

Structure-based search identifies homologous protein structures by comparing 3D conformations across databases like PDB and AlphaFold DB. Providing a query structure allows the system to rapidly retrieve a ranked list of similar structural hits.

Remote homolog detection for protein design scaffolds is best achieved through structural homology searching. By scanning against configured databases, this method uncovers distant evolutionary relationships that sequence-based searches often miss, providing viable scaffolds for design transfer.

Yes, you can perform structure-based clustering on a local collection of protein structures. By configuring the search to run against local databases, the tool groups structures by similarity, allowing for effective remote homolog detection and organization of local structural data.

Foldseek requires either local installation or web services to run structure searches. This flexibility allows users to configure databases and execute searches locally for large-scale data privacy or via web services for accessible, on-demand structural homology retrieval.

To get detailed alignment metrics and hit lists from a structure search, you provide a query structure and select a target database. The search outputs configurable formats containing comprehensive alignment data alongside a ranked list of structural hits.