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BioLiP weekly update download issue

Posted: Mon Jan 31, 2022 12:02 pm
by hevalatas

I am trying to download all BioLiP datasets via the Perl script given on the website. However, it gives an error message as "System call failed: at line 11.", and "cannot verify's certificate, issued by `/C=US/ST=MI/L=Ann Arbor/O=Internet2/OU=InCommon/CN=InCommon RSA Server CA'" is written in the log file. Is there a solution you can suggest for this problem?

I also wonder if it is possible to have downloadable lists of ligands based on their types (e.g. regular ligands, metal ligands, etc.). They are available on the website, but I couldn't find a way to download them with ligand-type information.

Another question is about the binding sites of proteins. Do you specify the type of binding sites (e.g., inhibition sites or allosteric sites), or do you involve all types of binding sites independently from its type?

As the last question, I wonder if you consider biological assemblies of PDB entries to identify binding sites for proteins that are functionally active only in macromolecular forms. In other words, do you involve binding sites of proteins in the form of macromolecules; if yes, do you map it for the biological assembly file of the corresponding protein or for its monomer form?

Thank you,

Re: BioLiP weekly update download issue

Posted: Mon Aug 08, 2022 4:32 am
by jlspzw
Dear user,

1 You can test re-download the library now

2 we didn't predict the specific type for binding sites.

3 No, we currently do not consider it.

IT team