LiveBench
Encyclopedia
LiveBench is a continuously running benchmark
project for assessing the quality of protein structure prediction
and secondary structure prediction
methods. LiveBench focuses mainly on homology modeling
and protein threading but also includes secondary structure prediction
, comparing publicly available webserver output to newly deposited protein structure
s in the Protein Data Bank
. Like the EVA
project and unlike the related CASP
and CAFASP
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.
Benchmark (computing)
In computing, a benchmark is the act of running a computer program, a set of programs, or other operations, in order to assess the relative performance of an object, normally by running a number of standard tests and trials against it...
project for assessing the quality of protein structure prediction
Protein structure prediction
Protein structure prediction is the prediction of the three-dimensional structure of a protein from its amino acid sequence — that is, the prediction of its secondary, tertiary, and quaternary structure from its primary structure. Structure prediction is fundamentally different from the inverse...
and secondary structure prediction
Secondary structure prediction
Secondary structure prediction is a set of techniques in bioinformatics that aim to predict the secondary structures of proteins and nucleic acid sequences based only on knowledge of their primary structure...
methods. LiveBench focuses mainly on homology modeling
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 protein...
and protein threading but also includes secondary structure prediction
Secondary structure prediction
Secondary structure prediction is a set of techniques in bioinformatics that aim to predict the secondary structures of proteins and nucleic acid sequences based only on knowledge of their primary structure...
, comparing publicly available webserver output to newly deposited protein structure
Protein structure
Proteins are an important class of biological macromolecules present in all organisms. Proteins are polymers of amino acids. Classified by their physical size, proteins are nanoparticles . Each protein polymer – also known as a polypeptide – consists of a sequence formed from 20 possible L-α-amino...
s in the Protein Data Bank
Protein Data Bank
The Protein Data Bank is a repository for the 3-D structural data of large biological molecules, such as proteins and nucleic acids....
. Like the EVA
EVA (benchmark)
EVA is a continuously running benchmark project for assessing the quality of protein structure prediction and secondary structure prediction methods...
project and unlike the related CASP
CASP
CASP, which stands for Critical Assessment of Techniques for Protein Structure Prediction, is a community-wide, worldwide experiment for protein structure prediction taking place every two years since 1994...
and CAFASP
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 recognition, and ab initio prediction of protein...
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.