[3dem] New version of PDB-IHM validation reports now include assessments of crosslinking mass spectrometry-based structure models

[Justin Flatt]

We are pleased to announce the release of updated validation reports 
(version 2) for structures determined using integrative and hybrid 
methods (IHM) archived in the PDB-IHM branch [1] of the PDB archive. 
These reports are available in the archive and on the PDB-IHM website 
[2]. IHM Validation software v2 is now integrated into the PDB-IHM 
deposition and curation system [3] to support validation of new 
depositions. For detailed information on IHM Validation and v2 updates, 
please refer to the help page [4] and user guide [5]. The software is 
also available for standalone use via GitHub [6].

We thank the wwPDB IHM Task Force [7] members and the broader structural 
biology community for supporting the development of validation methods 
for integrative structures.

WHAT’S NEW IN VERSION 2?

The latest update extends IHM validation to structures derived from 
Chemical Crosslinking Mass Spectrometry (Crosslinking-MS) data, in 
addition to the previously supported Small Angle Scattering (SAS) data. 
This milestone is the result of close collaboration among the 
Crosslinking-MS community, PRIDE [8] repository, and the PDB-IHM team.

To support this advancement, we have developed interoperability 
mechanisms between PDB-IHM and PRIDE, enabling validation of integrative 
structures based on Crosslinking-MS data. Additionally, PRIDE 
Crosslinking [9] now supports submission of complete Crosslinking-MS 
datasets following the mzIdentML 1.2.0 [10] community data standard.

Furthermore, IHM Validation software v2 uses MolProbity [11] version 
4.5.2 and the PrISM [12] software for precision analysis.

NEXT STEPS FOR DEPOSITORS

We encourage depositors working with Crosslinking-MS-based integrative 
structures to:

  	* Submit complete datasets to PRIDE Crosslinking following the 
provided guidelines [13].
  	* Cross-reference PRIDE Crosslinking datasets in PDB-IHM depositions 
to enable robust validation.



Links:
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[1] https://urldefense.com/v3/__https://files.wwpdb.org/pub/__;!!Mih3wA!BKQxgr_gwyBJqshCWyNe6q_dkpOqB-zSbWMpzy9oxDdQCx7-ED_YilWJC20p6076IQwLXllIs6XgdHLsJDcQRe_Y$ 
[2] https://urldefense.com/v3/__https://pdb-ihm.org/__;!!Mih3wA!BKQxgr_gwyBJqshCWyNe6q_dkpOqB-zSbWMpzy9oxDdQCx7-ED_YilWJC20p6076IQwLXllIs6XgdHLsJMbEtxRQ$ 
[3] https://urldefense.com/v3/__https://data.pdb-ihm.org/__;!!Mih3wA!BKQxgr_gwyBJqshCWyNe6q_dkpOqB-zSbWMpzy9oxDdQCx7-ED_YilWJC20p6076IQwLXllIs6XgdHLsJAOPJf8M$ 
[4] https://urldefense.com/v3/__https://pdb-ihm.org/about_validation.html__;!!Mih3wA!BKQxgr_gwyBJqshCWyNe6q_dkpOqB-zSbWMpzy9oxDdQCx7-ED_YilWJC20p6076IQwLXllIs6XgdHLsJF2xWCsZ$ 
[5] https://urldefense.com/v3/__https://pdb-ihm.org/validation_help.html__;!!Mih3wA!BKQxgr_gwyBJqshCWyNe6q_dkpOqB-zSbWMpzy9oxDdQCx7-ED_YilWJC20p6076IQwLXllIs6XgdHLsJNurTJ8a$ 
[6] https://urldefense.com/v3/__https://github.com/salilab/IHMValidation__;!!Mih3wA!BKQxgr_gwyBJqshCWyNe6q_dkpOqB-zSbWMpzy9oxDdQCx7-ED_YilWJC20p6076IQwLXllIs6XgdHLsJN_96JZp$ 
[7] https://urldefense.com/v3/__https://www.wwpdb.org/task/hybrid__;!!Mih3wA!BKQxgr_gwyBJqshCWyNe6q_dkpOqB-zSbWMpzy9oxDdQCx7-ED_YilWJC20p6076IQwLXllIs6XgdHLsJEc_I5x5$ 
[8] https://urldefense.com/v3/__https://www.ebi.ac.uk/pride/__;!!Mih3wA!BKQxgr_gwyBJqshCWyNe6q_dkpOqB-zSbWMpzy9oxDdQCx7-ED_YilWJC20p6076IQwLXllIs6XgdHLsJB57syIJ$ 
[9] https://urldefense.com/v3/__https://www.ebi.ac.uk/pride/archive/crosslinking__;!!Mih3wA!BKQxgr_gwyBJqshCWyNe6q_dkpOqB-zSbWMpzy9oxDdQCx7-ED_YilWJC20p6076IQwLXllIs6XgdHLsJLpn9YWE$ 
[10] 
https://urldefense.com/v3/__https://github.com/HUPO-PSI/mzIdentML/blob/master/schema/mzIdentML1.2.0.xsd__;!!Mih3wA!BKQxgr_gwyBJqshCWyNe6q_dkpOqB-zSbWMpzy9oxDdQCx7-ED_YilWJC20p6076IQwLXllIs6XgdHLsJPyMX8NM$ 
[11] https://urldefense.com/v3/__https://doi.org/10.1002/pro.3330__;!!Mih3wA!BKQxgr_gwyBJqshCWyNe6q_dkpOqB-zSbWMpzy9oxDdQCx7-ED_YilWJC20p6076IQwLXllIs6XgdHLsJGlM-shY$ 
[12] https://urldefense.com/v3/__https://doi.org/10.1093/bioinformatics/btac400__;!!Mih3wA!BKQxgr_gwyBJqshCWyNe6q_dkpOqB-zSbWMpzy9oxDdQCx7-ED_YilWJC20p6076IQwLXllIs6XgdHLsJDh3vrxi$ 
[13] https://urldefense.com/v3/__https://www.ebi.ac.uk/pride/markdownpage/crosslinking__;!!Mih3wA!BKQxgr_gwyBJqshCWyNe6q_dkpOqB-zSbWMpzy9oxDdQCx7-ED_YilWJC20p6076IQwLXllIs6XgdHLsJLLPOZoD$ 
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