Make your own free website on

Protein Visualization

The present project molpharm is running as part of M.S. project

From last one and half year i am doing Drug discovery related task as a java friend and lover of 3D world i thought making my own suit of molecular dynamics and docking which is in very primary step now.The visualization of the chemical information present in the files is the well known task in the chemoinformatics.So i started with it.At present my application MOLPHARM is able to visualize 13 types of file and convert them to each other.

Slide Show

Here is some of the figures from the Molpharm.The present status of the application is visualization.which support 13 file format.some of the popular file format are writen here.

MDL mol format=>*.mol
sybyl mol format=> *.mol2
xyz format=>*.xyz
PDB format=> *.PDB
mmCIF format=>*.mmcif
Chem draw file formats =>*.CDX
Alchemy file format => *.ALC etc
The application can read the files or directory for the particular file and convert then to the desire file format.The visualization also work for 7 file formats for visualization we have devlop an algorithm based on the one provided by rasmol.
Stick Model

The present technique of visualization uses our own algorithm which is prepared and tested on 600 molecules.The 3D library we are using is java3D and the jdk for the devlopment of the application.The present application is running on SGI ,Windows ,Linux etc.
Ball and Stick

This is again the protein from the PDB with the PDB ID 1pen the red ball remain unconnected are the water molecules and all other bonds are showing it's color accordingly.The appearance of the node is valid upto the atom and it's coresponding bonds so the nice picture of the bond half colored by the one bond and half by other suggesting the covalent bond.
Carbonlight Gray

The color values are taken from the literature after careful survey. This are then mapped to the color values in the java3D.
C alfa Trace

At present the number of the model supported are 6 which are shown in first diagram.The future devlopment is more towards the generation of the surfaces of the molecule by 5 algorithms which are under serious study and implementation of the molecular dynamics in more realistic and scientific way.