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/
