How to Use Protein Data Bank ¦ What is PDB ¦ PyMol Series ¦ Part 1 ¦ Basic Science Series Official

00:00 Introduction
00:41 Protein Data Bank
01:27 Example: LasR
02:52 Code
03:21 Using Code
03:42 Information
05:34 3D View
07:01 Options in 3D View
09:33 Annotations
09:45 Sequence
10:36 Experiment
11:03 Back to Home Page
11:28 Additional tools
11:54 Download the file
13:07 Conclusion

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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.

The PDB is key in areas of structural biologies, such as structural genomics. Most major scientific journals, and some funding agencies, now require scientists to submit their structure data to the PDB. Many other databases use protein structures deposited in the PDB. For example, SCOP and CATH classify protein structures, while PDBsum provides a graphic overview of PDB entries using information from other sources, such as Gene ontology.
PyMOL is an open-source molecular visualization system created by Warren Lyford DeLano. It was commercialized initially by DeLano Scientific LLC, which was a private software company dedicated to creating useful tools that become universally accessible to scientific and educational communities. It is currently commercialized by Schrödinger, Inc. PyMOL can produce high-quality 3D images of small molecules and biological macromolecules, such as proteins. According to the original author, by 2009, almost a quarter of all published images of 3D protein structures in the scientific literature were made using PyMOL

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