6533b861fe1ef96bd12c4fb4

RESEARCH PRODUCT

Experimental Evaluation of Protein Secondary Structure Predictors

Simona E. RomboGiuseppe TradigoPierangelo VeltriGiorgio TerracinaLuca MiceliLuigi Palopoli

subject

Protein structure databasebusiness.industryProtein structure predictionBioinformaticsMachine learningcomputer.software_genreSet (abstract data type)Bioinformatics Protein PredictionTest caseGlobal distance testArtificial intelligenceCASPbusinessPeptide sequencecomputerProtein secondary structure

description

Understanding protein biological function is a key issue in modern biology, which is largely determined by its 3D shape. Protein 3D shape, in its turn, is functionally implied by its amino acid sequence. Since the direct inspection of such 3D structures is rather expensive and time consuming, a number of software techniques have been developed in the last few years that predict a spatial model, either of the secondary or of the tertiary form, for a given target protein starting from its amino acid sequence. This paper offers a comparison of several available automatic secondary structure prediction tools. The comparison is of the experimental kind, where two relevant sets of proteins, a non-redundant one including 100 elements, and a 180-protein set taken from the CASP 6 contest, were used as test cases. Comparisons have been based on evaluating standard quality measures, such as the Q3 and SOV.

yearjournalcountryeditionlanguage
2009-01-01
https://doi.org/10.1007/978-3-642-01970-8_85