The Molecular Modeling Database (MMDB) is a database hosted by the National Center for Biotechnology Information that contains over 28,000 experimentally determined 3D structures of biomolecules including proteins and nucleic acids derived from the Protein Data Bank, excluding theoretical models. It facilitates computation and links structures to other data types. Each record cross-references its source PDB file. The database contains molecular structures, biological activity data, experimental data, chemical properties, and annotations to aid researchers. Examples of widely used molecular modeling databases discussed are the Protein Data Bank, PubChem, and RCSB Ligand Explorer.

1. MOLECULAR MODELING DATABASE
-Jayati Shrivastava

2. Molecular modeling database
The Molecular Modeling Database (MMDB) is a database of
experimentally determined three-dimensional biomolecular
structures and hosted by the National Center for
Biotechnology Information.
Over 28,000 3D macromolecular structures, including proteins
and polynucleotides

3. • 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.
• • The data processing procedure at NCBI results in the
addition of a number of useful features that facilitate
computation on the data and link them to many other data
types in the Entrez system.
• Each MMDB record cross-references the source PDB record
from which it was derived (i.e., the MMDB summary page
for a structure displays both its MMDB ID and the
corresponding PDB ID).
• If an MMDB record represents a structure that was merged
from two or more PDB split files, then the summary page
will show the PDB IDs

4. Content of molecular modeling database
• Molecular structures: The
database may contain
information about the atomic
coordinates of the molecule,
including the positions of
atoms, bonds, and functional
groups.

5. • Biological activity: The database may contain
information about the biological activity of the
molecule, such as its binding affinity to receptors,
enzyme inhibition, and toxicity.
• Experimental data: The database may contain
experimental data related to the molecular structure,
such as X-ray crystallography data, NMR spectra, and
mass spectrometry data.
Chemical properties: The database may contain
information about the chemical properties of
the molecule, such as melting point, boiling
point, solubility, and reactivity.

6. • Predictive modeling data: Some molecular modeling
databases may contain data related to predictive
modeling, such as molecular docking results, ligand-
protein interaction analysis, and molecular dynamics
simulations.
• Related data: Some molecular modeling databases may
contain related data, such as protein structures, gene
sequences, and other biological data that can help
researchers understand the molecular interactions
within a biological system.
Annotations and metadata: The database may contain
annotations and metadata, such as the source of the data,
the date of creation or modification, and information about
the molecule's origin, structure, and properties.

8. Examples of molecular modeling database
• Protein Data Bank (PDB): The PDB is a database
that stores three-dimensional structures of
proteins, nucleic acids, and complex assemblies. It
contains over 170,000 structures and is widely used
in molecular modeling and drug discovery research.

9. • PubChem: PubChem is a public database of
chemical substances, including small molecules and
bioassays. It contains information on over 100
million compounds and is a valuable resource for
drug discovery and chemical biology research.

10. • RCSB Ligand Explorer: The RCSB Ligand Explorer is
a web-based tool that allows users to search for
and visualize small molecule ligands in the PDB. It
provides detailed information on the ligand
structure, properties, and interactions with the
protein.

11. • ChemSpider: ChemSpider is a free chemical
structure database that provides access to over 100
million compounds. It is a useful resource for
chemists, biochemists, and molecular modelers
who need to search for and retrieve information on
chemical structures and properties.

12. • MolPort: MolPort is a commercial database of
chemical compounds that provides access to over 6
million compounds. It is primarily used by drug
discovery researchers and provides information on
compound availability, pricing, and supplier details.

13. How we can assess to molecular modeling
database?
Web-based interfaces: Many molecular modeling
databases provide web-based interfaces that allow users
to search, visualize, and analyze molecular data. These
interfaces are often freely accessible and require only an
internet connection and a web browser.
Software tools: Many molecular modeling databases
provide software tools that allow users to access the
database and perform computational analyses and
simulations. These tools are often free to download and
use, although some may require a license or subscription.

14. • Application rogramming Interfaces (APIs): Some
molecular modeling databases provide APIs that
allow developers to access the database
programmatically. This is useful for integrating the
database into other software tools and workflows.
• Data downloads: Some molecular modeling
databases provide downloadable data files that
contain the molecular structures and related data.
These files can be used with molecular visualization
software and other computational tools.

15. • Collaboration platforms: Some molecular modeling
databases provide collaboration platforms that
allow researchers to share data and collaborate on
research projects. These platforms often provide
additional features, such as data sharing, project
management, and communication tools.

16. Features of molecular modeling database
• Structure search: The ability to search for
molecular structures using a range of criteria, such
as molecular weight, functional groups, and
substructure searches.
• 3D visualization: The ability to visualize molecular
structures in 3D, allowing users to analyze the
structure and interactions between molecules.

17. • Chemical properties: The ability to retrieve a range
of chemical properties for a given molecule, such as
boiling point, melting point, and solubility.
• Biological activity: The ability to retrieve
information on the biological activity of molecules,
such as enzyme inhibition, receptor binding, and
toxicity.

18. • Experimental data: The ability to retrieve
experimental data related to the molecular
structure, such as X-ray crystallography data or
NMR spectra.
• Predictive modeling: Some molecular modeling
databases provide tools for predictive modeling,
such as molecular docking, ligand-protein
interaction analysis, and molecular dynamics
simulations.

19. • Access to related data: Many molecular modeling
databases provide access to related data, such as
protein structures, gene sequences, and other
biological data that can help researchers
understand the molecular interactions within a
biological system.
• Integration with other tools: Molecular modeling
databases often integrate with other software
tools and resources, such as molecular
visualization software, statistical analysis tools, and
bioinformatics resources.

20. Application of molecular modeling database
• Drug discovery: Molecular modeling databases are
extensively used in drug discovery to predict and
optimize the properties of potential drug
candidates. Researchers can use the database to
search for compounds with specific chemical
properties and biological activities, and then use
predictive modeling tools to optimize the molecular
structure to improve potency, selectivity, and
pharmacokinetic properties.

21. Materials science: Molecular modeling databases can be
used to design and optimize new materials, such as
polymers, nanoparticles, and catalysts. Researchers can use
the database to search for molecules with specific structural
and electronic properties, and then use predictive modeling
tools to simulate the behavior of the molecules in various
conditions.
Environmental science: Molecular modeling databases can
be used to study the behavior of pollutants, such as
pesticides and toxic chemicals, in the environment.
Researchers can use the database to search for molecules
with specific properties, and then use predictive modeling
tools to simulate the transport and fate of the molecules in
various environmental conditions.

22. • Protein engineering: Molecular modeling databases can be
used to design and optimize proteins with specific
properties, such as enzyme activity, binding affinity, and
stability. Researchers can use the database to search for
protein structures with similar folds and functional sites,
and then use predictive modeling tools to engineer new
proteins with improved properties.
• Biophysics: Molecular modeling databases can be used to
study the structure and function of biological
macromolecules, such as proteins, nucleic acids, and lipids.
Researchers can use the database to search for molecular
structures with specific properties, and then use predictive
modeling tools to simulate the behavior of the molecules in
various biological environments.