Bayesian Validation Subgroup Meeting
Jared Sagendorf
07/21/2023
IHM-Dictionary
Primary data format for archiving of integrative/hybrid structure models in PDB-Dev
Development of a Prototype System for Archiving Integrative/Hybrid Structure Models of Biological Macromolecules
B. Vallat, B. Webb, J. D. Westbrook, A. Sali and H. M. Berman
Structure 2018 Vol. 26 Issue 6 Pages 894-904.e2
Archiving and disseminating integrative structure models
B. Vallat, B. Webb, J. Westbrook, A. Sali and H. M. Berman
Journal of Biomolecular NMR 2019 Vol. 73 Issue 6-7 Pages 385-398
Dictionary browser: https://mmcif.wwpdb.org/dictionaries/mmcif_ihm.dic/Index/
IHM-Dictionary
Contents Overview
model representation
IHM-Dictionary
Extends model representation with coarse-grained spherical beads, three-dimensional Gaussian objects and other geometric primitives such as planes and tori.
Geometric Object Categories
IHM-Dictionary
Supports compositional and conformational heterogeneity and provides representations for multi-state structural models and models related by time or other order
B. Vallat, B. Webb, J. D. Westbrook, A. Sali, and H. M. Berman, Structure, vol. 26, no. 6, pp. 894-904.e2, 2018
IHM-Dictionary
Provides a general representation of spatial restraints and their uncertainties derived from different kinds of biophysical techniques.
Dihedral Restraint
Spatial Restraint
IHM-Dictionary
Provides a generic representation for cross-referencing related data from external resources via stable identifiers, such as accession codes or persistent digital object identifiers.
Model Representation
source: https://github.com/ihmwg/IHM-dictionary/blob/master/dictionary_documentation/documentation.md
Multi-scale
Multi-state
Ensembles
Ordered
Multi-Scale Model Representations
atomic model components
Multi-Scale Model Representations
multi-residue gaussian components
multi-residue spherical components
Models
models are collections of geometric objects representing various components of the system
Model Groups
Model groups act as arbitrary containers for groups of models. Their meaning is based on association with other data tables.
Multi-State Models
States are arbitrarily defined by the modeler and assigned to a model group. Act as meta-data on top of a model group
Ensembles
Ensembles are typically collections of structurally similar models, usually produced by clustering+filtering during the modeling process, but clustering information is not required
Data items in the IHM_ENSEMBLE_INFO category records the details of the model clusters or ensembles obtained after sampling.
Ordered
An ordered “ensemble” is just a directed graph of model groups
Data items in the IHM_ORDERED_ENSEMBLE category records the details of the ensembles ordered by time or other order. Ordered ensembles are described as directed graphs with edges between nodes representing models or model groups.
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B. Vallat, B. Webb, J. D. Westbrook, A. Sali, and H. M. Berman, Structure, vol. 26, no. 6, pp. 894-904.e2, 2018
Current Limitations