[3dem] [EXTERN] 3dem Digest, Vol 197, Issue 40

[Maryam Mohammadi]

Maryam Mohammadi | PhD Student | Braun Group Biozentrum, Spitalstrasse 41, 4056 Basel University of Basel  Tel mobile (preferred): +41 77 249 90 92  Tel Office:  (office): +41612076682
________________________________
From: 3dem <3dem-bounces at ncmir.ucsd.edu> on behalf of 3dem-request at ncmir.ucsd.edu <3dem-request at ncmir.ucsd.edu>
Sent: Tuesday, January 30, 2024 9:00:01 PM
To: 3dem at ncmir.ucsd.edu
Subject: [EXTERN] 3dem Digest, Vol 197, Issue 40

Send 3dem mailing list submissions to
        3dem at ncmir.ucsd.edu

To subscribe or unsubscribe via the World Wide Web, visit
        https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem
or, via email, send a message with subject or body 'help' to
        3dem-request at ncmir.ucsd.edu

You can reach the person managing the list at
        3dem-owner at ncmir.ucsd.edu

When replying, please edit your Subject line so it is more specific
than "Re: Contents of 3dem digest..."


Today's Topics:

   1. Preprint Published on NextGen Archive (Justin Flatt)


----------------------------------------------------------------------

Message: 1
Date: Tue, 30 Jan 2024 12:57:44 -0500
From: Justin Flatt <justin at rcsb.rutgers.edu>
To: 3dem <3dem at ncmir.ucsd.edu>
Subject: [3dem] Preprint Published on NextGen Archive
Message-ID: <c4e271068cc0c59b5cb482c16ff467d0 at rcsb.rutgers.edu>
Content-Type: text/plain; charset="us-ascii"; Format="flowed"

A new paper describes how the recently-announced NextGen Archive [2]
provides centralized access to integrated annotations and enriched
structural information for PDB data:

> NextGen Archive: Centralising Access to Integrated Annotations and
> Enriched Structural Information by the Worldwide Protein Data Bank
> Preeti Choudhary, Zukang Feng, John Berrisford, Henry Chao, Yasuyo
> Ikegawa, Ezra Peisach, Dennis W. Piehl, James Smith, Ahsan Tanweer,
> Mihaly Varadi, John D. Westbrook, Jasmine Y. Young, Ardan Patwardhan,
> Kyle L. Morris, Jeffrey C. Hoch, Genji Kurisu, Sameer Velankar, Stephen
> K. Burley
> (2023) _bioRxiv_ doi: 10.1101/2023.10.24.563739 [1]

The PDB NextGen archive [3] provides sequence annotation from external
resources such as UniProt, SCOP2 and Pfam in addition to the content
provided in the structure model files in the PDB main archive. The
inclusion of UniProtKB numbering facilitates effortless structural
comparisons between experimental and predicted protein models. These
PDBx/mmCIF files are directly compatible with various data visualization
tools, simplifying the display of annotations on 3D structure views.

Links:
------
[1] https://urldefense.com/v3/__https://doi.org/10.1101/2023.10.24.563739__;!!Mih3wA!GsD5mvMSewrySQ1-4s6JDtay6pNq9DcfKnAl8uQkqOm1tJwfgnwiR0Fq66GrEAH8VvkSu4BcMXpNrPzsjKEQJ5nR$
[2] https://urldefense.com/v3/__https://www.wwpdb.org/news/news?year=2023*63cedad9b5f08ee94ab73826__;Iw!!Mih3wA!GsD5mvMSewrySQ1-4s6JDtay6pNq9DcfKnAl8uQkqOm1tJwfgnwiR0Fq66GrEAH8VvkSu4BcMXpNrPzsjB8ezTYU$
[3] https://urldefense.com/v3/__https://www.wwpdb.org/ftp/pdb-nextgen-archive-site__;!!Mih3wA!GsD5mvMSewrySQ1-4s6JDtay6pNq9DcfKnAl8uQkqOm1tJwfgnwiR0Fq66GrEAH8VvkSu4BcMXpNrPzsjMSGlyuW$
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ncmir.ucsd.edu/pipermail/3dem/attachments/20240130/82b467b7/attachment-0001.html>

------------------------------

Subject: Digest Footer

_______________________________________________
3dem mailing list
3dem at ncmir.ucsd.edu
https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem


------------------------------

End of 3dem Digest, Vol 197, Issue 40
*************************************
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ncmir.ucsd.edu/pipermail/3dem/attachments/20240131/ece4f344/attachment.html>