SIMAP

Technical University of Munich, Center of Life and Food Sciences, Weihenstephan University of Vienna

SIMAP ( Similarity Matrix of Proteins, dt: the similarity matrix of proteins ) is a database for protein similarities. This database includes all previously published protein sequences and is continuously updated. Similarities of the proteins are calculated here using the FASTA algorithm. It is so far the only such database that actually involving all previously known proteins.

Background

Protein similarities are an important tool in bioinformatics. They provide a measure of a kind of kinship between different proteins. As the number of known proteins far exceeds the amount that can be studied experimentally in laboratories, the properties already investigated proteins to near relatives, so very similar proteins transferred. So far, these similarities were calculated anew again and again if necessary. In SIMAP these similarities are now completely calculated not on demand, but in advance and stored in the database. SIMAP is a joint project of the GSF Research Centre for Environment and Health in Neuherberg and the Technical University of Munich and is completely free for research and teaching available.

BOINCSIMAP

Since the immensely high computational effort exceeds the SIMAP capacity in predicting the similarities, it was decided, with the BOINCSIMAP project and access the SIMAP @ home program on means of distributed computing. To a client has been developed based on FASTA, which uses the BOINC infrastructure.

Another program called HMMER uses the Hidden Markov Model to search for protein domains, and is also sometimes used with BOINCSIMAP.

For the analysis of sequence similarities and domains among others, the data from the databases PDB, RefSeq, UniProt and GenBank are used.

In February 2014, the company Samsung Austria began to offer an app for the Android operating system under the name of Power Sleep, which offers the possibility of the computing power of smartphones during the night for this research project to provide. The app basically works on non - Samsung smartphones.