Thank you all for your valuable suggestions. On Mon, Oct 7, 2024 at 2:13 PM Robbie Joosten <robbie_joos...@hotmail.com> wrote:
> 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/ > -- *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 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/
