Software Facilities

In-House Software Development Activity 

To help the users from time to time, algorithms and programs are developed in the areas such as taxonomic classification, sequence analysis and structure prediction. A package for the production division of plant tissue culture industry is being developed. Similarly, general purpose programs for sequence analysis and molecular visualisation are developed in collaboration with the Centre for Development of Advanced Computing (C-DAC). These are PRAS, PNAS and MG which are marketed by C-DAC. Twenty copies of each of these programs are sold to various Universities and Research Institutions. Both the DOS and the transputer versions of these packages are available. It may be mentioned here that PRAS has received the BEST APPLICATION AWARD - "PARAM" instituted by C-DAC.

PRAS (Parallel Multiple Sequence Alignment Package)

There are three main computational modules viz. pairwise alignments of sequences, cluster analysis, profiling and collapsing of sequences. DOS version can simultaneously align 10 sequences upto 1000 characters each and the transputer version can align 100 sequences of 1000 characters.

The data and algorithmic parallelization is carried out efficiently to get almost a linear gain with an increase in the number of transputers. This is the first ever application of parallel processing to the multiple sequence alignment problem in the world.

PNAS (Protein and Nucleic Acid query System)

The PNAS allows analysis of protein and nucleic acid sequence data. This is a user-friendly package written in C and has all features that are available in most commercial packages. In addition, PNAS has several routines based on the methods developed in-house to analyse the sequence data. 

MG (Molecular Graphics)

This is the first Indian molecular visualization package that runs on the IBM compatible system. It allows the visualization of the molecules as ball and stick, ribbon and CPK in an user-friendly environment. It allows the manipulation of the molecules through rotation, zoom-in and out, calculation of geometrical parameters, protein and nucleic acid molecules can be built from its sequence information. 


MX - Molecular graphics and analysis software is an open ended molecular modelling software based on X - windows. This program displays molecules in wireframe, ball and stick, backbone and depth qued sphere representations. Graphics operations like rotation, translation, zooming, front and back clipping of the screen image is possible. The program also calculates all internal parameters of a molecule. For proteins (f ,Y ) angles are calculated and displayed in a Ramachandran plot. Other functions include an interface to secondary structure analysis program DSSP and a method based on Ca –Ca distance criteria developed in-house to decide the accuracy of predicted protein structure. The program can also help in creation of constraints file required for molecular simulations using AMBER. An energy minimizer that uses genetic algorithm is also available and that can be plugged in. 


X-windows based program to view nucleic acid molecular dynamics results in 'Dials and Windows' format. The program accepts pre-processed data from structure analysis programs like CURVES and generates dials and windows plots for their visualisation.
The program also gives two dimensional pseudo colour views of rms deviations.

Genetic Algorithms for Structure Prediction 

To predict three-dimensional structure of proteins and nucleic acids from their sequences, program based on Genetic Algorithms is being developed. This program is parallelised to obtain better efficiency, and works in PVM environment on the new PARAM system of C-DAC. 

Parallel AMBER and CHARMM on PARAM Open Frame

AMBER - Assisted Model Building with Energy Refinement program is widely used to carry out molecular dynamics studies of biopolymers in general and oligonucleotides in particular. Molecular Dynamics (MD) studies being compute intensive, molecules of biological interests are difficult to study even today. To overcome this hurdle the parallel version of AMBER was ported on the Indian Supercomputer PARAM Open Frame. The code which uses the farm field topology and dynamic load balancing, gave better benchmarking results on PARAM Open Frame with only eight nodes, than SPP (Scripps), SP2 (Cornell), T3D (Pittsburgh) and Cray-T90. This program was then used to carry out unconstrained MD studies on duplex of 13-mer oligonucleotide substrate of Pvull with the aim to gain an insight in the problem of mechanism of recognition and cleavage by type II endonucleases of DNA. MD studies, with only Watson-Crick base pairing constraint, were carried by immersing it in the water for 1 nano second at 283 k. Later simulations are also carried out for the same molecule in water with Na+ ions for 1.3 nano second at 283 k. To our knowledge such large simulations are not carried out anywhere in the world. Similarly, CHARMM- Chemistry at HARvard Molecular Mechanics is ported on parallel machine PARAM open frame. This work is carried out in collaboration with C-DAC. 

Multimedia Programs 

The first multimedia teaching-aid package in life sciences from India has been developed at our Centre on the "Immune System". The package is based on the windows environment using the Asymetrix Toolbook as the authoring software. The softwares like 3D studio, Animator Pro, CorelDraw, Photopoint video edit were also used to process images and animations. The present module of the package covers the overview of the immune system with a stress on fundamentals of immunology. 

Application Software

Molecular Modelling 


CURVES : Structural analysis of nucleic acids 
InSight II (Biosym) : Ampac/Mopac, Biopolymer, Builder, DelPhi,Discover, DMol, Viewer modules 
JUMNA : Building and minimization of nucleic acids 
NAMOT : Modelling of nucleic acids 
X-PLOR : A system for X-ray crystallography and NMR 


AMBER : Molecular Modelling with energy minimization routines and dynamics 
MX : X-windows based graphics and analysis program 
MxCurv : X-windows based graphics program to view Nucleic acid dynamics results in 'Dials & windows' format 
SOPM : Consensus secondary structure prediction using the available prediction methods 


NAMD : Parallel program for molecular dynamics 
Parallel AMBER : Parallel version of AMBER 
CHARMM : Parallel version of CHARMM 


DTMM : DeskTop Molecular Modeller 
MG : Molecular Graphics package : 
PCM : PC Modeller 
RASMOL : Molecular modelling package 

Sequence Analysis Programs


Unix Based 


Taxonomic Classification


Statistical Packages

PC Base

Teaching Aid Packages



Medical Physiology

Computer Fundamentals