PDB@ Help Center
Welcome to the PDB tutorial center…!!!!
Here we will look into few basic ways of accessing PDB@ and extracting information from it.
1.
INSTALLATION and DOWNLOAD of PERL and various other PERL modules.
The following are the PERL modules that will be required to work with PDB@. a.
WWW::Mechanize b.
Tk::Checkbutton c.
Tk::BrowseEntry d.
Tk::TableMatrix e.
Tk::TableMatrix::Spreadsheet f.
Tk::Table g.
Tk::LabFrame h.
List::Util qw(max) i.
List::Util qw(min) j.
Bio::Structure::IO
To install these PERL modules please go to the following link: http://www.bribes.org/perl/ppmdir.html
To download the above modules find the respective module name in the list of given modules. For e.g.: Tk::TableMatrix is available in the list:

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On selecting the module please check the compatibility version of PERL which will be displayed on the right end of the same row as of the name of the module.
Copy the link specified for the respective module and paste in in your Command Prompt and hit Enter.
Upon installation of the module you will get a message like this
In case there is any problem in installation please check your net connectivity or your
PERL compatibility. If the same problem still persists please enter the same link in your command prompt but with a “ --force” keyword before the link

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2.
WORKING with PDB@:
Upon installation of all the modules please change the current working directory to the directory where the main program ( PDB@.pl
) is present in your hard disk.
Enter the command perl PDB@.pl
to run the program.
This is the main homepage of the tool. The following are the various modules available for utility. a.
FAST PDB b.
Miscellaneous Properties c.
Graphical Viewer d.
Utilities e.
Property Calculations f.
Ramachandran Explorer g.
PDB Editor
FAST PDB: Users are required to specify a text file with a list of PDB ID’s to download.
On submission PDB@ will itself download all the files from RSCB PDB and save it in a new directory in the working directory.
For the remaining utilities users are required to upload a PDB file into the tool
(4HHB.pdb)

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Upon uploading the PDB file you will be displayed with the following screen
Multi chain alignment
Input PDB file
Amino acid statistics
MISCELLANEOUS PROPERTIES: In this section users are provided with further more options such as: a.
SHEETS : Used to select the sheet regions between a specific range of amino acids b.
HELIX: Used to select the helix regions between a specific range of amino acids c.
Selector: Used to specifically select the Standard or Nonstandard residues.
Users can also select CA, side chain or Backbone atoms. d.
HetraAtom: Displays the HETATM details of the PDB file. e.
FASTA Converter: Converts the PDB file into FASTA file.
Sample output from the Helix option.

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GRAPHICAL VIEWER: Users are given 5 different options in this section a.
Heat Map b.
Hydrophobicity Graph c.
Dot Plot d.
Mobility Graph e.
Property Graph
Sample outputs:
Heat Map
Hydrophobicity Graph

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Dot Plot
Mobility Graph
UTILITIES: Here users are offered 3 different options a.
RMSD for conformers: Users are required to upload 2 PDB files that are same but conformers of each other. This option helps in identifying the RMSD between them.
b.
PSA calculator: Protein Surface Area calculator. c.
Protein – Ligand distance: Displays the distance between a HETATM and a particular chain in the PDB file. A specific region can also be mentioned.

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PROPERTY CALCULATIONS: There 6 sub options in the category a.
Region separator: Splits the entire PDB file into SSE (helix, sheet and disordered regions based on the Phi (θ) and Psi (Ψ) angles) b.
Interactions: Identifies the Disulphide, Ionic, Cation – Pi, Polar and Salt
Bridges in the PDB file.
c.
Distance calculation: Cα – Cα, Cβ – Cβ and distance between 2 atoms.
d.
Ligand distance: Distance between each atom in the PDB file to the ligand in the PDB file.
e.
Radius of Gyration f.
Center of Mass
Region Separator
RAMACHANDRAN EXPLORER: This option can be used to identify the Phi (θ) and Psi
(Ψ) angles of atoms of a particular chain. The atoms are also plotted onto the
Ramachandran Plot. A slider has been used to diminish the number of atoms to a particular range. For e.g.: To identify the Phi (θ) and Psi (Ψ) angles of amino acids in the
A chain with their angles between -108 o to +180 o .

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The slider must be placed in such a fashion.
PDB EDITOR: Here the user must again upload his PDB file. Here we will take the example of PDB file 1T8A.pdb
Options such as a.
Search: To search for the ATOM that has C, N and O as the Elementary atom.
We also can search for a particular residue. E.g.: Search for the residue MET in the A chain. Users must first click on A chain -> ATOM -> Search -> Residue search. Type MET in the entry box and click search.

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Deletion: Atom based deletion and Residue based deletion.
c.
Insert: Insertion of a row can be done before or after an atom.
d.
Co-ordinate replace: The X, Y and Z co-ordinates of a particular residue can be altered.
NOTE: At any time the output obtained can be saved and used for further analysis.
For further clarifications or doubts please contact the Email-Id’s provided in the Help
Center website: http://www.bioindians.org/PDB .