As discussed briefly in the article Structural Bioinformatics , the Protein Data Bank (PDB) is a remarkable asset in structural biology. The PDB is a database of the atomic structure of proteins, and some other macromolecules like nucleic acids, that biologists and biochemists have compiled for the use of other scientists, students and the general public. The primary information stored in this database is called “coordinate files” which show each atom’s spatial location within the three-dimensional structure of the macromolecule. This atomic composition is experimentally generated by methods such as X-ray crystallography, cryo-electron microscopy and NMR spectrophotometry. Accompanying the image of the structure is also the primary sequence, chemistry, functional structure (termed biological assembly) and the function of the macromolecule, if each is known. Often, each macromolecule is accompanied by primary literature or an article written by an expert in the field.
The need for a protein database became evident in the early 1970’s as protein crystallography and three-dimensional structure became more advanced and popular within the field of biology. At that time, only a select few laboratories had exchanged coordinates, what is now known as coordinate files, on single cards. This meant that a protein with one thousand atoms required one thousand cards, a very inefficient and complex way of exchanging information. By 1971, Walter Hamilton, a chemist working to determine the structure of amino acids, with the help of other experts in the field established the Protein Data Bank in collaboration with the Cambridge Crystallographic Data Center and Brookhaven National Laboratory. Shortly after in 1974, PDB had 13 structures in its database. Today, the PDB has over 93,000 structures.
Quick Guide to Using PDBEdit
PDB can be used in two ways:
a) To search for specific macromolecules, sequences or ligands to primarily determine atomic and 3D structure. Here's what happens when I did a basic search:
I searched for the mammalian target of rapamycin (mTOR) under macromolecules in the search bar shown in Figure 1.This brought me to a page that if I scrolled down, I would find a list of articles related to mTOR. I chose this link as shown in Figure 2. It provided me with information about the article itself, including the location in PubMed , the molecular description and the structural image.
b) To investigate different macromolecules of interest through PDB-101, written in a more relaxed article style immediately relevant to human life (Figure 3). Here one can find interesting current topics in the field such as this month's Molecule of the Month, designed protein cages. If one is interested in the structure of the molecule, it is easy enough to click on the picture and choose the desired image (cartoon, ball and stick, ligans and pocket, etc). In addition, these molecules can also have PDB entries which contain more detailed information on the structure.
Berman, Helen. "The Protein Data Bank: a historical persceptive". 2007. http://www.ebi.ac.uk/msd/embo08/pdf/pdb_history.pdf
The Protein Data Bank. http://www.rcsb.org/pdb/home/home.do
"The Protein Data Bank". Wikipedia. http://en.wikipedia.org/wiki/Protein_Data_Bank </li>