Uppsala Software Factory - Other programs

• QDB is a program to query a database containing statistics and quality information for 476 X-ray protein structures. The program is available via ftp.

• ALPHABET - to investigate secondary structure of triplets of amino acids using a database. This may be useful when designing mutations that should not disrupt the secondary structure. The program can also be used to predict secondary structure, but in my experience, it works best for predicting the *absence* of such (i.e., loop regions). Not available.

• PREDIC - predict CA geometry of a protein given its sequence, using a database. The tertiary predictions are crap, but parts of the secondary structure are sometimes predicted correctly. Not available.