Structural databases of bioinformatics

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MOLECULAR MODELLING DATABASE (MMDB) 
MMDB contain experimental data from crystallography and NMR structure 
determinations. The data from MMDB are obtained from the PDB. 
The NCBI has cross linked structural data to bibliographic information, to the sequence 
databases, and to the NCBI taxonomy. The Molecular Modelling Database (MMDB) is 
a database of experimentally determined three-dimensional bimolecular structures, and 
is also referred to as the Entrez Structure database. It is a subset of three-dimensional 
structures obtained from the RCSB Protein Data Bank (PDB), excluding theoretical 
models. Most structure data are obtained from X-ray crystallography and NMR-
spectroscopy. X-ray crystallography determines the arrangement of atoms within a 
protein by passing X-rays through a crystallized form of the protein and analysing the 
resulting X-ray diffraction pattern. This technique provides the highest resolution and 
usually yields only one model of a structure. Nuclear magnetic resonance 
(NMR) determines the structure of a protein in solution and generally yields multiple 
models, which allow for characterization of the bio molecule
’s motion in solution. 
An example of each type of structure is shown in the section of this document on 
"record types", and additional experimental methods are listed in the Method search 
field 
of 
the 
database. 
As an alternative to these experimental methods, some researchers use computational 
modelling to predict the structure of a protein by simulating the forces that act on each 
atom in a molecule of known composition. However, this method produces non-
experimental models and the least reliable results. For these reasons, the Molecular 
Modelling Database excludes computationally generated structures or other theoretical 
models and includes only experimentally determined structures.