Need a link to OLDERADO server

Question

[b2003]

I want to access a server OLDERADO: On-line database of ensemble representatives and domains

this is the link to the article: https://onlinelibrary.wiley.com/doi/10.1002/pro.5560061215

However, the link provided inside the article to direct us to the server isn't working, I tried looking up "OLDERADO" online but I just couldn't find it, Was the link changed? and if so what is the new one?

[GenoMax]

This paper is from 1997 and as with many academic tool instances this one has likely gone to the tool heaven. You are going to be better off looking for a current alternative.

[b2003]

It shouldn't be gone though, it was cited in multiple papers in 2020-2021-2022

[GenoMax]

The link included in the paper is no longer working today, as you discovered. You could try emailing the senior author and ask. Please post an update if you hear back about a new location.

[Wayne]

It was at http://www.ebi.ac.uk/msd-srv/pqs/pqs-nmr.html according to this page on 'NMR Ensembles of Models' Proteopedia.
That now redirects to PDBePISA. It has been doing that since about 2016 according to the Internet Wayback Machine.

The Version Log for PDBePISA says for Version 1.11 23/04/2007:

Added analysis of custom assemblies given As Is by coordinate section in PDB or mmCIF files. This analysis does not use crystal descriptions, therefore it is applicable to NMR structures. The results are found in the "assemblies" section.

That is all I could find concerning NMR and PDBePISA. I don't know if that means it covers what OLDERADO did. I haven't used PDBePISA for NMR, only crystal structures.

[b2003]

would this tool allow me to find the average/most representative NMR model?

[Wayne]

I don't know quite why it goes there. More about that below...
(Maybe more puzzling is why you have such recent papers citing it since my information from the Wayback Machine didn't have it available since around 2016? Maybe it was assumed that was the source of some data since it had been in the past. Or someone was using old datasets? "cited in multiple papers in 2020-2021-2022" isn't exactly providing a lot of detail.)

I do think that PDB generally now offers what that server used to cover.

Quote at RCSB here:

NMR structures are commonly deposited as ensembles of structures. The best representative model is made available as the “Assembly” coordinates.

The NMR files I have looked at all have 'Biological Assembly 1' that you can download. On the summary page, if you click the arrow to cycle the structure image summary on the left side off 'NMR Esemble' to 'Biolgical Assembly 1', you'll see notes like "Biological assembly 1 assigned by authors."

Examples:

• 1lcd , that you can download at https://files.rcsb.org/download/1LCD.pdb1.gz (Note: OCA lists that same file name for 'Biological Unit Coordinates' on the OCA page for 1lcd.)
• 2n3q , that you can download at https://files.rcsb.org/download/2N3Q.pdb1.gz (Note:OCA lists that same file name for 'Biological Unit Coordinates' on the OCA page for 2n3q.)

I'm wondering if it forwards to PDBePISA because both involve 'assemblies' these days? I'm unclear on the reasoning, or even if there was any. Is that just the default if a tool goes away that was hosted at EMBL-EBI?

On the NMR ensembles, you may want to look at here, too:

You should check the comments on the PDB file. If the authors don't call out a specific model as being the best representative of the family, then you can usually assume that it is the first one. The authors have access to the underlying constraint data that you do not have.

[b2003]

Alright I'll check that thread, thanks