Related Experiment Video
Updated: Aug 15, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction
Published on: November 3, 2011
SIMAP--the similarity matrix of proteins
Roland Arnold1, Thomas Rattei, Patrick Tischler
1Institute for Bioinformatics, GSF-National Research Center for Environment and Health Ingolstädter, Neuherberg, Germany.
Motivation:
Sequence similarity searches are of great importance in bioinformatics. Exhaustive searches for homologous proteins in databases are computationally expensive and can be replaced by a database of pre-calculated homologies in many cases. Retrieving similarities from an incrementally updated database instead of repeatedly recalculating them should provide homologs much faster and frees computational resources for other purposes.
Results:
We have implemented SIMAP-a database containing the similarity space formed by almost all amino acid sequences from public databases and completely sequenced genomes. The database is capable of handling very large datasets and allows incremental updates. We have implemented a powerful backbone for similarity computation, which is based on FASTA heuristics. By providing WWW interfaces as well as web services, we make our data accessible to the worldwide community. We have also adapted procedures to detect putative orthologs as example applications.
Availability:
The SIMAP portal page providing links to SIMAP services is publicly available: http://mips.gsf.de/services/analysis/simap/. The web services can be accessed under http://mips.gsf.de/proj/hobitws/services/RPCSimapService?wsdl and http://mips.gsf.de/proj/hobitws/services/DocSimapService?wsdl
Related Concept Videos
Protein Networks
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Protein Organization
The primary structure of a protein is its amino acid sequence.
Protein Organization
Conservation of Protein Domains Over Different Proteins
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
Conserved Binding Sites
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Protein-protein Interfaces

