PDB-Dev and Integrative/Hybrid (I/H) Modeling
PDB-Dev is a prototype deposition and archiving system for structural models obtained
through integrative/hybrid (I/H) methods.
Structures of complex macromolecular assemblies are difficult to obtain from a single
structure determination method such as X-ray crystallography (X-ray), NMR spectroscopy
(NMR) and Electron microscopy (3DEM).
In such cases, a combination of complementary experimental and computational techniques
are used to determine the structures. These methods are collectively called as integrative/hybrid
(I/H) methods. In addition to X-ray crystallography, NMR, and 3DEM, methods such as small angle
scattering (SAS), atomic force microscopy (AFM), chemical cross-linking (CX), co-purification,
Förster resonance energy transfer (FRET), electron paramagnetic resonance (EPR), mass spectrometry (MS),
H/D exchange (HDX), and various proteomics and bioinformatics techniques are part of I/H modeling
methods. Spatial restraints derived from the different kinds of experimental and computational methods
are combined to derive the structure of the macromolecular assembly.
Integrative/hybrid (I/H) methods have been applied to determine the structures of assemblies such as
the nuclear pore complex and its sub-complexes, the type III secretion system needle,
the proteosomal lid sub-complex, the ESCRT-I complex, and an RNA ribosome-binding element
from the turnip crinkle virus genome.
We have developed a data dictionary for archiving structural models
of macromolecular assemblies derived through integrative/hybrid methods.
The I/H methods dictionary defines
the data specifications required for archiving the I/H structural models, the associated
spatial restraints and structural model computation protocols. This dictionary
is a logical, modular extension of the PDBx/mmCIF dictionary
currently used by the wwPDB for archiving atomic structures of macromolecules.
The new dictionary extension addresses two
fundamental requirements of I/H methods: (a) descriptions of spatial restraints
derived from a variety of experimental techniques and
(b) definitions of multi-scale, multi-state, and time-ordered ensembles of macromolecular
assemblies. A general representation of multi-scale models together with the
experimentally determined spatial restraints is an important feature of the new I/H
The current I/H methods dictionary and associated documentation can be found
The wwPDB consortium has established an integrative/hybrid methods
task force to tackle the many issues involved in
archiving models determined by integrative/hybrid methods.
This task force comprises of experts in the various experimental fields that contribute
to the development of integrative/hybrid methods, along with experts in structural and computational biology, and
experts in archiving. The PDB-Dev prototype system is developed based on the recommendations made by the
wwPDB I/H methods task force published in a white paper
(Sali et al., Structure. 2015 Jul 7; 23(7):1156-1167; doi:
PDB-Dev and the I/H methods dictionary are being developed by a multi-disciplinary team of researchers and developers from the
wwPDB and the
I/H methods task force.
The list of contributors can be found here.