Similarity Matrix of Proteins, or SIMAP, is a database of protein similarities created using distributed computing, which is freely accessible for scientific purposes. SIMAP uses the FASTA algorithm to precalculate protein similarity, while another application uses hidden Markov models to search for Protein domains.
The database has now been completed, but will be updated for newly discovered proteins.
SIMAP uses the Berkeley Open Infrastructure for Network Computing (BOINC) distributed computing platform.
Application performance notes:
- Work unit CPU times can vary widely, ranging between 15 minutes and 3 hours.
- Work units are around 600 KB to 1.35 MB each, averaging around 1.20 MB.
- SIMAP provides client software optimized for SSE enabled processors. For older processors non SSE applications are provided but require manual installation steps to be taken. Operating Systems supported by SIMAP are Linux, Windows, Mac OS and other UNIX platforms.
- Since the database has been completed, there will be only sporadic work available in the near future.