PDB - an introduction to a common term in structural biology

(1) The PDB is the Protein Data Bank, a single worlwide repository for 3D structural data of biological molecules.

(2) A PDB is a file, typically with a "pdb" file extension, contains 3D structural data of a particular biological molecule. In short, a PDB file is broken into two sections: (i) a header that contains much background information on the molecule in question such as authors and experimental conditions, (ii) 3D coordinate data that contain the vital experimental data in the form of 3D cartesian coordinates, B-factors, atom information, and more.

How can PDBs be Visualized?

Protein Data Bank files, containing some form of macromolecular coordinate set, are visualized via graphic computing. A myriad of advanced molecular visualization programs are used in academic and industrial setting, and some of these are specific to the field of research or the techniques used to collect the coordinate data. For example, X-ray crystallographers use O, XtalView, MAIN, or other programs for crystallographic modeling. These allow the researcher to model the coordinate set into the electron density from the collected X-ray data.

However, PDB files are "final" deposited coordinates. This means that the depositor has made their best effort to provide a final model that is as accurate as they could make it. Programs like Molscript, Pymol, SwissPDBview/DeepView, Molmol, SETOR, DINO and others are routinely used to visualize deposited coordinates.

In order to produce molecular graphics, one requires the following: graphics workstation computer, some form of molecular graphics software, and most importantly, training.

Symmation has been formally trained in X-ray crystallography and bioinformatics. We have the software and computer equipment, aside from our 8 years of experience. We are able to provide a complete solution to molecular graphics visualization that includes raw data interpretation, remodeling, refinement, structure analysis, and of course publication-quality graphics.

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