CASP, which stands for Critical Assessment of Techniques for Protein Structure Prediction, is a community-wide experiment (though it is commonly referred to as a competition) for protein structure prediction taking place every two years. Protein structure prediction is one of the most significant tasks tackled in computational structural biology and theoretical chemistry. ...
CASP provides research groups with an opportunity to assess the quality of their methods for protein structure prediction from the primary structure of the protein. As a consequence, CASP provides the research community with an assessment of the state of the art in this field. Protein structure prediction is one of the most significant tasks tackled in computational structural biology and theoretical chemistry. ... A protein primary structure is a chain of amino acids. ...
Protein structures that have been recently resolved, but not yet published, are used as targets for the evaluation. If the given sequence is found (for example, using sequence alignment methods such as BLAST or FASTA) to be similar to a protein sequence of known structure, comparative protein modelling may be used to predict the tertiary structure. Otherwise, other methods such as protein threading or de novo protein structure prediction must be applied. The results of CASP are published [1] and are divided into several prediction categories: Sequence alignment is an arrangement of two or more sequences, highlighting their similarity. ... In bioinformatics, Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing biological sequences, such as the amino-acid sequences of different proteins or the DNA sequences. ... FASTA is a sequence alignment package first described (as FASTP) by David J. Lipman and William R. Pearson in 1985 in the article Rapid and sensitive protein similarity searches. ... In biochemistry, the tertiary structure of a protein is its overall shape. ... Protein structure prediction is one of the most significant tasks tackled in computational structural biology. ...
secondary structure prediction (as of CASP5 this field was dropped)
homology modelling
fold recognition (also called protein threading; Note, this is incorrect as threading is a method.)
contact prediction
de novo structure prediction Now referred to as 'New Fold' as many methods apply evaluation, or scoring, functions that are biased by knowledge of native protein structures, such an example would be an artificial neural network.
function prediction
Protein structure prediction is one of the most significant tasks tackled in computational structural biology. ... Protein structure prediction is one of the most significant tasks tackled in computational structural biology. ...
The signalling problem addressed by CASP is the same as the overall problem being addressed by the NSIS activities, for which a set of requirements are given in [1] and an outline framework in [2].
A CASP client can, however, send back responses that allow the client which sent a message to confirm that the initial message was delivered and to determine whether the operation was successful or encountered an error.
A CASP message consists of a common header, followed by a body consisting of a variable number of variable-length objects, which are identified as being of a particular type.
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