Dear all,
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*
<https://files.wwpdb.org/pub/> of the PDB archive. These reports are
available in the archive and on the *PDB-IHM website*
<https://pdb-ihm.org/>. IHM Validation software v2 is now integrated
into the PDB-IHM *deposition and curation system*
<https://data.pdb-ihm.org/> to support validation of new depositions.
For detailed information on IHM Validation and v2 updates, please refer
to the *help page* <https://pdb-ihm.org/about_validation.html> and *user
guide* <https://pdb-ihm.org/validation_help.html>. The software is also
available for standalone use via *GitHub*
<https://github.com/salilab/IHMValidation>.
We thank the *wwPDB IHM Task Force*
<https://www.wwpdb.org/task/hybrid> 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*
<https://www.ebi.ac.uk/pride/> 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* <https://www.ebi.ac.uk/pride/archive/crosslinking> now
supports submission of complete Crosslinking-MS datasets following the
*mzIdentML 1.2.0*
<https://github.com/HUPO-PSI/mzIdentML/blob/master/schema/mzIdentML1.2.0.xsd> community
data standard.
Furthermore, IHM Validation software v2 uses *MolProbity*
<https://doi.org/10.1002/pro.3330> version 4.5.2 and the *PrISM*
<https://doi.org/10.1093/bioinformatics/btac400> 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*
<https://www.ebi.ac.uk/pride/markdownpage/crosslinking>.
* Cross-reference PRIDE Crosslinking datasets in PDB-IHM depositions
to enable robust validation.
Read this news online:
https://www.wwpdb.org/news/news?year=2025#67c4575365ecc77724b625ed
Kind regards,
Deborah Harrus, on behalf of the wwPDB
########################################################################
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list
hosted by www.jiscmail.ac.uk, terms & conditions are available at
https://www.jiscmail.ac.uk/policyandsecurity/
