Molecular Modeling Database

Molecular Modeling Database (MMDB) is a comprehensive database that provides data on three-dimensional biomolecular structures, including proteins, nucleic acids (such as DNA and RNA), and polysaccharides. These structures are primarily determined through X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, and cryo-electron microscopy. The MMDB is part of the National Center for Biotechnology Information (NCBI) suite of databases, which is a crucial resource for researchers in the fields of bioinformatics, molecular biology, and computational chemistry.

Overview

The MMDB contains detailed information on the 3D structures of molecules, including atomic coordinates, structural classifications, and links to related literature and biological data. It is integrated with other NCBI databases, such as GenBank for genetic sequences and PubMed for scientific publications, allowing for comprehensive searches that connect genetic information, biological function, and structural data.

Data Acquisition and Processing

Structural data in the MMDB are primarily sourced from the Protein Data Bank (PDB), the global repository for biomolecular structures. Upon inclusion, the data undergoes processing and annotation by NCBI staff to ensure accuracy and to add value through the integration with other NCBI resources. This process includes the assignment of Conserved Domain Database (CDD) annotations, which highlight important structural and functional motifs within the molecules.

Features and Tools

The MMDB offers a variety of tools and features for researchers:

• 3D Viewer: A tool for the visualization of structures within the browser, allowing users to rotate, zoom, and explore molecular structures interactively.
• Structure Alignment: Users can compare the 3D structures of different molecules to identify structural similarities and differences.
• Link to Cn3D: A downloadable software provided by NCBI for more advanced visualization and analysis of biomolecular structures.
• Integrated Search: The ability to perform searches based on sequence or structural similarity, linking directly to related genetic and literature information.

Applications

The MMDB is used in a wide range of scientific and educational fields. Researchers utilize the database for drug design and discovery, understanding protein function and interaction, and studying the genetic basis of diseases. Educators and students use MMDB as a resource for teaching and learning about molecular biology and biochemistry.

Challenges and Future Directions

Despite its extensive utility, the MMDB faces challenges such as keeping pace with the rapidly increasing volume of structural data and integrating new types of biomolecular structures. Future developments may focus on enhancing the database's usability, expanding its content, and improving integration with other databases and computational tools.

See Also

• Protein Data Bank (PDB)
• National Center for Biotechnology Information (NCBI)
• X-ray crystallography
• Nuclear magnetic resonance (NMR) spectroscopy
• Cryo-electron microscopy

Molecular Modeling Database Resources
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