Memory-efficient, accelerated protein interaction inference with blocked, multi-GPU D-SCRIPT.
basic_science · Level V
Where this comes from
- Record sourced from PubMed, PMID 41075159.
- Also identified by DOI 10.1093/bioinformatics/btaf564 and PMC identifier 12553328.
- Licence recorded as CC BY.
- The licence permits redistribution, so the abstract is shown in full and the full text is available from the publisher.
Abstract
D-SCRIPT is a powerful tool for high-throughput inference of protein-protein interactions (PPIs), but it is expensive in time and memory to infer all PPIs for network-/proteome-level analyses. We introduce D-SCRIPT with blocked multi-GPU parallel inference, which substantially reduces memory usage across tasks and computational systems (13.8× for a representative large proteome) and enables multi-GPU parallelism. Blocked multi-GPU parallel inference has been integrated into the main D-SCRIPT package, available at https://github.com/samsledje/D-SCRIPT. An archived version of the code at time of submission can be found at https://doi.org/10.5281/zenodo.16325182.
Medical subject headings
- Software
- Protein Interaction Mapping
- Computational Biology