STAMP (structural alignment of multiple proteins) for comparison, superimposition and alignment of protein three-dimensional structures. Allows one to compare a singe protein domain to a database of others to detect similarities not obvious from sequence. For information on getting STAMP click here or click here to read the on-line manual and here to read the abstract from the paper. Similarities between several proteins have been detected using STAMP, including that between SH2 domains and BirA, between HIV matrix protein p17 and gamma interferon, between catalase and calycins and several others
ASSP (Accuracy of Secondary Structure Prediction) Takes a multiple sequence alignment and estimates the lower limit in accuracy one should expect for a perfect consensus secondary structure prediction based on the alignment. Accompanies a paper written in J. Mol Biol.