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<div id="x_divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> 3dem <3dem-bounces@ncmir.ucsd.edu> on behalf of 3dem-request@ncmir.ucsd.edu <3dem-request@ncmir.ucsd.edu><br>
<b>Sent:</b> Tuesday, January 30, 2024 9:00:01 PM<br>
<b>To:</b> 3dem@ncmir.ucsd.edu<br>
<b>Subject:</b> [EXTERN] 3dem Digest, Vol 197, Issue 40</font>
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Today's Topics:<br>
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1. Preprint Published on NextGen Archive (Justin Flatt)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Tue, 30 Jan 2024 12:57:44 -0500<br>
From: Justin Flatt <justin@rcsb.rutgers.edu><br>
To: 3dem <3dem@ncmir.ucsd.edu><br>
Subject: [3dem] Preprint Published on NextGen Archive<br>
Message-ID: <c4e271068cc0c59b5cb482c16ff467d0@rcsb.rutgers.edu><br>
Content-Type: text/plain; charset="us-ascii"; Format="flowed"<br>
<br>
A new paper describes how the recently-announced NextGen Archive [2] <br>
provides centralized access to integrated annotations and enriched <br>
structural information for PDB data:<br>
<br>
> NextGen Archive: Centralising Access to Integrated Annotations and <br>
> Enriched Structural Information by the Worldwide Protein Data Bank<br>
> Preeti Choudhary, Zukang Feng, John Berrisford, Henry Chao, Yasuyo <br>
> Ikegawa, Ezra Peisach, Dennis W. Piehl, James Smith, Ahsan Tanweer, <br>
> Mihaly Varadi, John D. Westbrook, Jasmine Y. Young, Ardan Patwardhan, <br>
> Kyle L. Morris, Jeffrey C. Hoch, Genji Kurisu, Sameer Velankar, Stephen <br>
> K. Burley<br>
> (2023) _bioRxiv_ doi: 10.1101/2023.10.24.563739 [1]<br>
<br>
The PDB NextGen archive [3] provides sequence annotation from external <br>
resources such as UniProt, SCOP2 and Pfam in addition to the content <br>
provided in the structure model files in the PDB main archive. The <br>
inclusion of UniProtKB numbering facilitates effortless structural <br>
comparisons between experimental and predicted protein models. These <br>
PDBx/mmCIF files are directly compatible with various data visualization <br>
tools, simplifying the display of annotations on 3D structure views.<br>
<br>
Links:<br>
------<br>
[1] <a href="https://urldefense.com/v3/__https://doi.org/10.1101/2023.10.24.563739__;!!Mih3wA!GsD5mvMSewrySQ1-4s6JDtay6pNq9DcfKnAl8uQkqOm1tJwfgnwiR0Fq66GrEAH8VvkSu4BcMXpNrPzsjKEQJ5nR$">
https://urldefense.com/v3/__https://doi.org/10.1101/2023.10.24.563739__;!!Mih3wA!GsD5mvMSewrySQ1-4s6JDtay6pNq9DcfKnAl8uQkqOm1tJwfgnwiR0Fq66GrEAH8VvkSu4BcMXpNrPzsjKEQJ5nR$</a>
<br>
[2] <a href="https://urldefense.com/v3/__https://www.wwpdb.org/news/news?year=2023*63cedad9b5f08ee94ab73826__;Iw!!Mih3wA!GsD5mvMSewrySQ1-4s6JDtay6pNq9DcfKnAl8uQkqOm1tJwfgnwiR0Fq66GrEAH8VvkSu4BcMXpNrPzsjB8ezTYU$">
https://urldefense.com/v3/__https://www.wwpdb.org/news/news?year=2023*63cedad9b5f08ee94ab73826__;Iw!!Mih3wA!GsD5mvMSewrySQ1-4s6JDtay6pNq9DcfKnAl8uQkqOm1tJwfgnwiR0Fq66GrEAH8VvkSu4BcMXpNrPzsjB8ezTYU$</a>
<br>
[3] <a href="https://urldefense.com/v3/__https://www.wwpdb.org/ftp/pdb-nextgen-archive-site__;!!Mih3wA!GsD5mvMSewrySQ1-4s6JDtay6pNq9DcfKnAl8uQkqOm1tJwfgnwiR0Fq66GrEAH8VvkSu4BcMXpNrPzsjMSGlyuW$">
https://urldefense.com/v3/__https://www.wwpdb.org/ftp/pdb-nextgen-archive-site__;!!Mih3wA!GsD5mvMSewrySQ1-4s6JDtay6pNq9DcfKnAl8uQkqOm1tJwfgnwiR0Fq66GrEAH8VvkSu4BcMXpNrPzsjMSGlyuW$</a>
<br>
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