I agree with Randy about the secondary structure things. The main use of HSSP in my hand is having ready-made multiple sequence alignments that allow you to quickly check the distribution of residues at a specific position: this glycine is 100% conserved in 1337 sequences, I guess it is rather important.
Anyway, HSSP is indeed offline but I have the last version of the databank for anyone who wants it (mail me off-list). A problem with HSSP was that it was rather maintenance-heavy for the number of users. If it becomes obvious that there is strong demand for it, may reappear. Cheers, Robbie > -----Original Message----- > From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> On Behalf Of Randy > John Read > Sent: Monday, October 7, 2024 10:26 > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] re- HSSP Database > > Maybe someone else will have a different opinion, but I suspect that the very > best method to predict secondary structure at the moment is to predict the > tertiary structure using AlphaFold or another machine-learning structure > prediction method, and then observe the secondary structure in the predicted > structure. These machine-learning methods have clearly learned how to > generalise from homology to known structures, evolutionary covariance, and > probably other aspects of protein structure. > > Best wishes, > > Randy Read > > > On 7 Oct 2024, at 08:24, Bhavita Kattula <bhavit...@gmail.com> wrote: > > > > Hello everyone, > > I'm trying to access the Homology-derived Secondary Structure of Proteins > (HSSP) database for protein structure-sequence alignments, but I am > encountering issues. The database does not seem to be functioning as expected, > and I'm unable to retrieve the necessary data. > > Could anyone confirm whether this is a temporary issue or if there are > ongoing maintenance or updates taking place? Additionally, I would greatly > appreciate recommendations for alternative databases that provide similar > functionalities, particularly for accessing protein structure-sequence > alignments > and related data. > > > > Best wishes, > > -- > > Bhavita Kattula > > Graduate student > > C/o Dr. Anthony Addlagatta > > Chief Scientist > > Structural Biology Lab > > CSIR-Indian Institute of Chemical Technology, > > Tarnaka, Hyderabad-500007. > > > > To unsubscribe from the CCP4BB list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > ----- > Randy J. Read > Department of Haematology, University of Cambridge > Cambridge Institute for Medical Research Tel: +44 1223 336500 > The Keith Peters Building > Hills Road E-mail: > rj...@cam.ac.uk > Cambridge CB2 0XY, U.K. > www-structmed.cimr.cam.ac.uk > > ################################################################### > ##### > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing > list hosted by www.jiscmail.ac.uk, terms & conditions are available at > https://www.jiscmail.ac.uk/policyandsecurity/ ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
