LiveBench is a continuously running
benchmark project for assessing the quality of
protein structure prediction
Protein structure prediction is the inference of the three-dimensional structure of a protein from its amino acid sequence—that is, the prediction of its secondary and tertiary structure from primary structure. Structure prediction is differen ...
and
secondary structure prediction methods. LiveBench focuses mainly on
homology modeling
Homology modeling, also known as comparative modeling of protein, refers to constructing an atomic-resolution model of the "''target''" protein from its amino acid sequence and an experimental three-dimensional structure of a related homologous p ...
and
protein threading
Protein threading, also known as fold recognition, is a method of protein modeling which is used to model those proteins which have the same fold as proteins of known structures, but do not have homologous proteins with known structure.
It differs ...
but also includes
secondary structure prediction, comparing publicly available
webserver
A web server is computer software and underlying hardware that accepts requests via HTTP (the network protocol created to distribute web content) or its secure variant HTTPS. A user agent, commonly a web browser or web crawler, in ...
output to newly deposited
protein structure
Protein structure is the molecular geometry, three-dimensional arrangement of atoms in an amino acid-chain molecule. Proteins are polymers specifically polypeptides formed from sequences of amino acids, the monomers of the polymer. A single ami ...
s in the
Protein Data Bank
The Protein Data Bank (PDB) is a database for the three-dimensional structural data of large biological molecules, such as proteins and nucleic acids. The data, typically obtained by X-ray crystallography, NMR spectroscopy, or, increasingly, c ...
. Like the
EVA project and unlike the related
CASP and
CAFASP CAFASP, or the Critical Assessment of Fully Automated Structure Prediction, is a large-scale blind experiment in protein structure prediction that studies the performance of automated structure prediction webservers in homology modeling, fold recog ...
experiments, LiveBench is intended to study the accuracy of predictions that would be obtained by non-expert users of publicly available prediction methods. A major advantage of LiveBench and EVA over CASP projects, which run once every two years, is their comparatively large data set.
References
* Bujnicki JM, Elofsson A, Fischer D, Rychlewski L. (2001). LiveBench-1: continuous benchmarking of protein structure prediction servers. ''Protein Sci'' 10(2):352-61.
* Rychlewski L, Fischer D. (2005). LiveBench-8: the large-scale, continuous assessment of automated protein structure prediction. ''Protein Sci'' 14(1):240-5.
External links
LiveBench main site
{{bioinformatics-stub
Bioinformatics
Protein methods