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HSSP / Homology-derived Secondary Structure of Proteins
Consists of a derived database merging information from three-dimensional structures and one-dimensional sequences of proteins. HSSP is a resource of aligned sequence families, but also a database of implied secondary and tertiary structures. It can be useful for analyzing residue conservation in structural context, for defining structurally meaningful sequence patterns and, in general, for studying protein evolution, folding and design.
The polyproline helix type II (PPII) is a regular protein secondary structure with remarkable features. Many studies have highlighted different crucial biological roles supported by this local conformation, e.g. in the interactions between biological macromolecules. Although PPII is less frequently present than regular secondary structures such as canonical alpha helices and beta strands, it corresponds to 3–10% of residues. Up to now, PPII is not assigned by most popular assignment tools, and therefore, remains insufficiently studied. PolyprOnline database is, therefore, dedicated to PPII structure assignment and analysis to facilitate the study of PPII structure and functional roles.
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 structures in the Protein Data Bank (PDB). 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.
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