Molecule Tutorials - Herong's Tutorial Examples
∟PDB (Protein Data Bank)
∟What Is PDB (Protein Data Bank)
This section provides a quick introduction of the PDB (Protein Data Bank), which is a database for the three-dimensional structural data of large biological molecules, such as proteins and nucleic acids.
What Is PDB (Protein Data Bank)? -
The Protein Data Bank (PDB) is a database for the three-dimensional structural data
of large biological molecules, such as proteins and nucleic acids. The data,
typically obtained by X-ray crystallography, NMR spectroscopy, or, increasingly,
cryo-electron microscopy, and submitted by biologists and biochemists from around
the world, are freely accessible on the Internet via the websites of its member
organizations (PDBe, PDBj, RCSB, and BMRB). The PDB is overseen by an organization
called the Worldwide Protein Data Bank, wwPDB.
PDB related Websites include:
- http://www.wwpdb.org -
Website for the Worldwide PDB (wwPDB) organization which manages
the PDB archive and ensures that the PDB is freely and publicly available to the global community.
- http://www.rcsb.org -
Website for the RCSB PDB (Research Collaboratory for Structural Bioinformatics Protein Data Bank),
which provides simple and advanced searching for macromolecules and ligands, tabular reports,
specialized visualization tools, sequence-structure comparisons, RCSB PDB Mobile, Molecule of
the Month and other educational resources at PDB-101, and more.
- https://www.ebi.ac.uk/pdbe/ -
Website for the PBDe (Protein Data Bank in European),
which provides rich information about all PDB entries, multiple search and browse facilities,
advanced services including PDBePISA, PDBeFold and PDBeMotif, advanced visualization
and validation of NMR and EM structures, tools for bioinformaticians.
- https://pdbj.org -
Website for the PBDj (Protein Data Bank Japan)
which supports browsing in multiple languages such as Japanese, Chinese, and Korean;
SeSAW identifies functionally or evolutionarily conserved motifs by locating
and annotating sequence and structural similarities, tools for bioinformaticians, and more.
- http://www.bmrb.wisc.edu -
Website for the BMRB (Biological Magnetic Resonance Data Bank),
which Collects NMR (Nuclear Magnetic Resonance) data from any experiment and captures assigned chemical
shifts, coupling constants, and peak lists for a variety of macromolecules;
contains derived annotations such as hydrogen exchange rates, pKa values,
and relaxation parameters.
Table of Contents
About This Book
Introduction of Molecules
Molecule Names and Identifications
Molecule Mass and Weight
Protein and Amino Acid
Nucleobase, Nucleoside, Nucleotide, DNA and RNA
Gene and Chromosome
Protein Kinase (PK)
DNA Sequencing
Gene Mutation
SDF (Structure Data File)
PyMol Installation
PyMol GUI and CLI
PyMol Selections
PyMol Editing Functions
PyMol Measurement Functions
PyMol Movie Functions
PyMol Python Integration
PyMol Object Functions
ChEMBL Database - European Molecular Biology Laboratory
PubChem Database - National Library of Medicine
►PDB (Protein Data Bank)
►What Is PDB (Protein Data Bank)
What Is CRSB (Research Collaboratory for Structural Bioinformatics)
What Is PDBe (Protein Data Bank in Europe)
What Is PDBj (Protein Data Bank Japan)
VR molecular viewer by PDBj
INSDC (International Nucleotide Sequence Database Collaboration)
HGNC (HUGO Gene Nomenclature Committee)
Relocated Tutorials
Resources and Tools
Molecule Related Terminologies
References
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