SIMAP@Home Project

From Unofficial BOINC Wiki

SIMAP (Similarity Matrix of Proteins) - http://boinc.bio.wzw.tum.de/boincsimap/ - SIMAP (Similarity Matrix of Proteins) is a public database of pre-calculated protein similarities that plays a key role in many bioinformatics methods. Protein sequence comparison is the most powerful tool in computational biology for characterizing protein sequences because of the enormous amount of information that is preserved throughout the evolutionary process.

Contents 1 General 2 Status of the Project 3 Reading List for Protein Folding Related Projects 4 More About SIMAP@Home 5 Also See

[edit] General

The SIMAP@Home Project, a BOINC Powered Project is in its last testing stage (Beta Test) at the moment.

The SIMAP@Home Project computes the Similarity Matrix of Proteins SIMAP, a publicly available resource to investigate and to utilize similarities between protein sequences. Similarities between two protein sequences imply a common evolutionary origin, also called homology. If two proteins are probably homologs, it is quite likely that they share a similar three-dimensional fold and, importantly, might have the same or similar functionality. The SIMAP@Home Project uses a Science Application called the "SIMAP Computation Application" which is used to precompute these similarities in an all-against-all approach using the Fasta algorithm. SIMAP allows convenient access by different interfaces as the web-interface and web-services for researchers all around the world.

SIMAP speeds up analysis wherever homology detection plays a role. It is therefore a valuable resource for many different kinds of biological/bioinformatical analysis and may give additional insights since it allows to investigate the whole 'protein space' at once or in user-defined parts.

The SIMAP system itself is maintained by the Chair of Comparative Genome Research at the Technical University of Munich (TUM) and developed in cooperation with MIPS/IBI, the Munich Institute for Protein Sequences (MIPS/IBI) at the GSF research center for environment and health.

[edit] Status of the Project

Currently, the first Work Units have been computed. Some problems still remain and have to be solved, for example: the stability of the Linux-client. The generation process of the Work Units has been changed in order to generate Results of moderate size.

[edit] Reading List for Protein Folding Related Projects

Regrettably, there is somewhat confusing vocabulary necessary to begin a discussion of the Rosetta@Home method of protein folding, as well as comparisons of this approach with other related BOINC Powered Projects: Poem@Home, Folding@Home, Predictor@Home, Rosetta@Home, SIMAP@Home, and World Community Grid.

• Proteins
• Protein Structure
• Protein Folding

[edit] More About SIMAP@Home

• Getting started with SIMAP@Home
• SIMAP@Home FAQ
• The Science Behind SIMAP@Home
• What Is The Difference Between The Different Protein Projects; Including Folding@Home, Predictor@Home, Rosetta@Home, SIMAP, and World Community Grid?
• How much resource share should I give to SIMAP@Home?
• More about the SIMAP@Home Science
• In-built Visualization/Screensaver
• Problems Running - How-To Test Machine Stability

[edit] Also See

The SIMAP web-interface at MIPS.