The Pfam database is a large collection of multiple sequence alignments and hidden Markov models covering many common protein domains. T.K. Attwood et al., Nucleic Acid Research, 2000. Scordis P, Flower DR, Attwood TK, Bioinformatics. Chaperon is a neural network program capable of correlated predictions by employing multiple output units. The neural network activities for output units are also reported making judgment about the reliability possible.
Predator is a secondary structure prediction program available for non-commercial use.
It is based on recognition of potentially hydrogen-bonded residues and involves database derived statistics for specific residue types. It is well known in secondary and tertiary structure prediction studies that the performance can be greatly improved by incorporating evolutionary information. For this purpose and for the value per se we also list a profile calculated from multiple sequence alignments. The profile is the frequency of occurrence of each of the 20 standard amino acids in each position of the alignment. The format of the profile is similar to the HSSP profile format except that we currently list only the profile values not the quality indices.