Computer in Science: Protein Data Bank

What is Protein Data Bank (PDB)?

Biologists and biochemists use sequence databases, structure databases, literature databases, etc. The database we will learn here is called the Protein Database (PDB). The PDB has all known 3D structures of proteins, DNAs and RNAs. To find the PDB on the web, type ‘PDB’ into google, and go to the first link returned, which is http://www.rcsb.org/pdb/home/home.do

You need to download the protein structures (i.e., the PDB files) that you are going to study, to your own computer. Each structure is in a pdb file with a name that does not carry much information (for example 1H97.pdb). A PDB file is a simple text file with the xyz coordinates of all the atoms in the protein (one protein has lots and lots of atoms).

Search for the protein that you want to study, for example, Neuraminidase

Scroll down to find the specific protein

Download the file by clicking PDB File(text)

The data format that PDB use is macromolecular crystallographic information file (mmCIF). It been introduced in the late 1990's. As the result,PDB has been very useful for every kind of human being,especially scientist,lecturers and students. These are 5 examples of the proteins that have been downloaded:

1) Neuraminidase

2) ClpP

3) HtrA

4) Trypsin

5) Subtilisin

Name	Neuraminidase	ClpP	HtrA	Trypsin	Subtilisin
Molecule Name	der Influenza-Neuraminidase-Teil 2	Escherichia coli	Putative serine protease	Erythrina Trypsin Inhibator	Serine endopeptidase
Classification	Hydrolase	Hydrolase	Protein binding	Proteinase Inhibator	Protease
Type	Protein	Protein	Protein	Protein	Protein
Length	388	193	134	172	269

Now, what software or program shall we use to open such file? This is when Rasmol comes into rescue!

What is RasMol ?
RasMol is a program for molecular graphics visualisation originally developed by Roger Sayle. This site is provided for the convenience of users of RasMol and developers of open source versions of Rasmol. It is a free program which displays molecular structure.
RasMol was designed for viewing protein structures -- molecules so large that one would not make an ordinary molecular model by hand. However, it can also be used for small molecules. Using RasMol for small molecules is particularly useful if you do not have a set of models. If you do have models, it may be good to learn to use RasMol with small molecules, and even compare the RasMol model with the "physical" models.
To get started with RasMol :

1. Open file of RasMol: File/Open from within RasMol. From within Netscape, click on a RasMol viewable molecule (a .pdb file). (RasMol should automatically start and load in the molecule.)