IHMValidation

IHMValidation assesses integrative hybrid structure models by providing quality assessments and data fit evaluations for PDB-IHM entries based on recommendations from structural biology communities.

Key Features:

• Quality Assessment Reports: Generates comprehensive validation reports in PDF and HTML formats comprising six sections: overview, model details, data quality assessments, local geometry assessments, fit of the model to data used to generate it, and fit of the model to data used for validation.
• Multi-Community Recommendations: Incorporates recommendations from the wwPDB Integrative Methods Task Force, small-angle scattering (SAS), chemical crosslinking mass spectrometry (crosslinking-MS), and cryo-electron microscopy and tomography (3DEM) communities.
• Multi-Scale and Multi-State Support: Evaluates structure models with multi-scale and multi-state representations derived from 17 types of experimental data.

Scientific Applications:

• Integrative Structure Model Validation: Validates integrative/hybrid structure models deposited to PDB-IHM, a branch of the Protein Data Bank that expands scope to additional biomolecular structure representations and experimental information types.
• Data Quality and Consistency Assessment: Assesses underlying data quality and consistency with input data for rigorous interpretation of structure models archived in the PDB.
• Positional Uncertainty Evaluation: Provides estimates of positional uncertainty of structure model components.

Methodology:

The pipeline evaluates data quality, local geometry, and model-to-data fit for both data used to generate the model and data used for validation.