Dear Yuan Shang,
HSSP provides multiple sequence alignments with conservation scores per position. It is originally PDB derived in the sense that a multiple sequence alignment already exists for each PDB entry. You can also make HSSP entries from sequence alone, but you should contact the HSSP maintainers because Iā m not sure this service is public yet. You can also cheat a bit and just get the HSSP for the closest homologue in the PDB. HTH, Robbie Joosten Netherlands Cancer Institute From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of ?? Sent: Wednesday, August 22, 2012 06:17 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] protein sequence database with conservation score annotation Hi,everyone, Does anyone here could recommend such a database for me? I've searched the web and only find tools like 'consurf'. Databases like 'consurf' are important for the analysis of the current known structures. However, for the original discoveries of new domains, sequence databases with such conservation score annotation could be as important as the secondary structure prediction. Although the 'conservation score' maynot be as accurate as that from the 'consurf database' which is based on the 3-D alignment. The information of such database could be much more helpful, especially for some new proteins, or proteins regions without any structure available. Best regards, Yuan SHANG HKUST
