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    Anwesha Mazumder

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    Atm Abhay Sharma
    The document discusses several popular molecular structure databases including PubChem, Chem-Spider, Cambridge Structural Database, Protein Data Bank, and Chemical Entities of Biological Interest. It then provides more details about the Protein Data Bank, describing it as a repository of three-dimensional protein and nucleic acid structures, and highlighting its features of structural data, quality control, and search/analysis tools. The document also discusses the Structural Classification of Proteins database and CATH database, describing their classifications of protein domains and structures.

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    Anwesha Mazumder

    Uploaded by

    Atm Abhay Sharma
    7 views12 pages
    The document discusses several popular molecular structure databases including PubChem, Chem-Spider, Cambridge Structural Database, Protein Data Bank, and Chemical Entities of Biological Interest. It then provides more details about the Protein Data Bank, describing it as a repository of three-dimensional protein and nucleic acid structures, and highlighting its features of structural data, quality control, and search/analysis tools. The document also discusses the Structural Classification of Proteins database and CATH database, describing their classifications of protein domains and structures.

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    ANWESHA MAZUMDER PPT

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    The document discusses several popular molecular structure databases including PubChem, Chem-Spider, Cambridge Structural Database, Protein Data Bank, and Chemical Entities of Biological Interest. It then provides more details about the Protein Data Bank, describing it as a repository of three-dimensional protein and nucleic acid structures, and highlighting its features of structural data, quality control, and search/analysis tools. The document also discusses the Structural Classification of Proteins database and CATH database, describing their classifications of protein domains and structures.

    Copyright:

    © All Rights Reserved
    Download as PDF, TXT or read online from Scribd
    Download as pdf or txt
    7 views12 pages

    Anwesha Mazumder

    Uploaded by

    Atm Abhay Sharma
    The document discusses several popular molecular structure databases including PubChem, Chem-Spider, Cambridge Structural Database, Protein Data Bank, and Chemical Entities of Biological Interest. It then provides more details about the Protein Data Bank, describing it as a repository of three-dimensional protein and nucleic acid structures, and highlighting its features of structural data, quality control, and search/analysis tools. The document also discusses the Structural Classification of Proteins database and CATH database, describing their classifications of protein domains and structures.

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    of 12

    JAIPUR NATIONAL UNIVERSITY

    Molecular Structure Databases


    PROTEIN DATA BANK(PDB), SCOP,CATH.
    COURSE:- BSC [Hons] MICROBIOLOGY
    SUBMITTED BY- ANWESHA MAZUMDER [4th Semester]
    SUBMITTED TO- ANKITA SINGH
    Molecular Structure Database
    Molecular structure databases are essential tools for researchers in chemistry, biochemistry, and
    related fields for understanding the properties and behavior of molecules.

    Some popular molecular structure databases include:

    ➢PubChem

    ➢Chem-Spider

    ➢Cambridge Structural Database (CSD)

    ➢Protein Data Bank (PDB)

    ➢Chemical Entities of Biological Interest (ChEBI)

    ➢Re-axys
    Protein Data Bank (PDB)
    The Protein Data Bank (PDB) is a comprehensive and widely used repository of
    three-dimensional structural data for large biological molecules, primarily
    proteins and nucleic acids.
    It provides a wealth of information about the shapes and conformations of these
    molecules, as well as their interactions with other molecules, such as drugs and
    ligands.
    Protein Data Bank (PDB)
    Key features of the Protein Data Bank include:

    Repository of Structural Data

    Quality Control

    Search and Analysis Tools


    Protein Data Bank (PDB)
    ➢Repository of Structural Data: The PDB is the single global repository for
    three-dimensional structures of biological macromolecules, such as proteins,
    nucleic acids, and complex assemblies.
    ➢Quality Control: This includes checks for stereochemical quality, geometric
    parameters, and validation against experimental data.
    ➢Search and Analysis Tools: The PDB provides users with advanced search and
    analysis tools to explore the database efficiently. Users can search for structures
    based on various criteria, such as molecule type, resolution, experimental
    method, and sequence similarity.
    Structural Classification Of Proteins (SCOP)
    The Structural Classification of Proteins (SCOP) is a hierarchical classification of
    protein structural domains.
    It aims to provide a comprehensive and systematic organization of protein
    structures, allowing researchers to explore relationships between protein
    sequences, structures, and functions.
    The Structural Classification of Proteins (SCOP) serves several important
    functions in the field of structural biology and bioinformatics:
    Structural Classification Of Proteins (SCOP)
    Key features of the SCOP include:

    Classification and Organization

    Identification of Structural Similarities

    Understanding Protein Evolution


    Structural Classification Of Proteins (SCOP)
    Key features of the SCOP include:
    ➢Classification and Organization: SCOP classifies and organizes protein
    structures into a hierarchical framework based on their structural and
    evolutionary relationships.
    ➢Identification of Structural Similarities: SCOP helps identify structural
    similarities between proteins that may not be apparent from sequence alone.
    ➢Understanding Protein Evolution: SCOP aids in the study of protein evolution
    by organizing proteins into evolutionary groups based on structural similarities.
    CATH (Class, Architecture, Topology,
    Homology)
    The CATH (Class, Architecture, Topology, Homology) database is a
    comprehensive resource for the classification and analysis of protein structures. It
    provides a hierarchical classification of protein domains based on their structural
    and evolutionary relationships.
    CATH (Class, Architecture, Topology,
    Homology)
    Key features of the CATH include:

    Classification of Protein Domains

    Topology Identification

    Education and Training


    CATH (Class, Architecture, Topology,
    Homology)
    Key features of the CATH include:
    ➢Classification of Protein Domains: CATH categorizes protein domains into
    hierarchical levels based on their structural features, including Class,
    Architecture, Topology, and Homologous Superfamily.
    ➢Topology Identification: The Topology level in CATH describes the spatial
    arrangement of secondary structural elements within protein domains.
    ➢Education and Training: These resources include tutorials, workshops, and
    online courses aimed at both beginners and advanced users, helping to improve
    understanding and utilization of protein structure classification data.

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