Molecule Tutorials - Herong's Tutorial Examples
∟PDB (Protein Data Bank)
∟What Is CRSB (Research Collaboratory for Structural Bioinformatics)
This section provides a quick introduction of the CRSB (Research Collaboratory for Structural Bioinformatics, which is a member organization of Worldwide PDB (wwPDB).
What Is CRSB (Research Collaboratory for Structural Bioinformatics)? -
CRSB is a member organization of Worldwide PDB (wwPDB).
It 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.
Main features of CRSB include:
- Search by Chemical Formula or Descriptor -
Use Advanced Search>Chemical Search for small-molecule searching by formulae or descriptors (SMILES, InChI)
- Updated Validation Reports for Released PDB Structures -
Reports now include recalculated percentiles, 2D diagrams highlighting ligand quality, map and model fit for EM entries, and calculated map coefficients used for X-ray data validation.
- Explore Sequence-Structure Relationships -
Protein Feature View maps PDB structures and corresponding UniProtKB sequences and other annotations in an updated interface
- Real Time Structural Search of the PDB -
A new paper describes a novel method that detects similarity between protein shapes and that works equally fast for any size of proteins or assemblies
- Access Improved Carbohydrate Data at the PDB -
A new data representation for carbohydrates in PDB entries and reference data improves the Findability and Interoperability of these molecules in macromolecular structures. Lists of PDB entries, CCDs, PRDs, and non-PDB compatible entries are available.
- Integrating PDB Data with NIH Common Fund Data Resources -
Access information from PHAROS (important drug target protein families: GPCRs, ion channels and kinases), GTEx (tissue-specific gene expression and regulation) and IMPC (data related to mouse phenotypes).
- Introducing a New Molecular Display -
Using Mol* for 2D image generation gives a more modern look
- Sequence Motif Searching -
Use Advanced Search to find short sequence patterns in PDB structures
- Enter the Coronavirus CellPAINT Contest -
Show us how you can illustrate coronavirus with a new version of CellPAINT
For more information on PRCSB, visit
https://www.rcsb.org Website.
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
Full Version in PDF/EPUB