Milot Mirdita

Abstract Detecting similar protein structural motifs in large structure collections is computationally expensive. We developed Folddisco, a fast structural motif search tool that uses an index of position-independent geometric features, including side-chain orientation, combined with a rarity-based scoring system. Folddisco is 20-fold faster in querying and fourfold more storage-efficient than existing methods while improving accuracy.

Editor’s summary Protein structures can preserve information about evolutionary relationships that are no longer possible to detect by sequence alone. However, aligning by structure is computationally intensive, and with the advent of large-scale structure prediction, there is a need for tools that can efficiently align vast numbers of structures. Gilchrist et al. present FoldMason, a tool designed for this purpose that is based on parallelized progressive alignment.

Abstract Rapidly growing protein databases demand faster sensitive search tools. Here the graphics processing unit (GPU)-accelerated MMseqs2 delivers 6× faster single-protein searches than CPU methods on 2 × 64 cores, speeds previously requiring large protein batches.