PDB-IHM Validation System

Welcome to the PDB-IHM Validation System.

This server performs the same validation as you would observe during the deposition process. This service is designed to help you check your model and experimental files prior to start of deposition.

Validation reports are generated based on guidelines and recommendations from IHM TaskForce (Berman et al. 2019). The current version of the PDB-IHM validation report consists of five categories, (i) overview, (ii) model details, (iii) data quality assessments, (iv) model quality assessments, and (v) fit to data used to build the model. A sixth category, fit to data used to validate the model is under development. Data quality assessments and fit to data used for modeling categories are dependent on the different types of experimental data used in integrative modeling. We are breaking down this section based on experimental data type and addressing each method separately. The current version of the validation report is focused on validating models built using Small Angle Scattering (SAS), Chemical Crosslinking Mass Spectrometry (crosslinking-MS), and 3D Electron Microscopy (3DEM) data and is based on the model and data validation guidelines published by the wwPDB SAS validation task force (Trewhella et al., 2017), crosslinking-MS (Leitner et al., 2020), and 3DEM communities (Kleywegt et al., 2024).

Use the links below to start exploring the system:

Please report problems to ihmv@pdb-ihm.org.