Software and Databases
 Lectin Database
Lectins, a class of carbohydrate binding proteins are now widely recognized to play a range of crucial roles in many cell-cell recognition events triggering several important cellular processes. They encompass different members that are diverse in their sequences, structures, binding site architectures, quaternary structures, carbohydrate affinities and specificities as well as their larger biological roles and potential applications.
It is not surprising therefore that the vast amount of experimental data on lectins available in the literature is so diverse, that it becomes difficult and time-consuming, if not impossible to comprehend the advances in various areas and obtain the maximum benefit.
In order to achieve an effective use of all the data towards understanding the function and their possible applications, an organization of these seemingly independent data into a common framework is essential. An integrated knowledge base (Lectindb) together with appropriate analytical tools has therefore been developed initially for plant lectins by collating and integrating diverse data.
The database has been implemented using MySQL on a Linux platform and web-enabled using Perl-CGI and Java tools. Data for each lectin pertains to taxonomic, biochemical, domain architecture, molecular sequence and structural details as well as carbohydrate and hence blood group specificities. Extensive links have also been provided for relevant bioinformatics resources and analytical tools. Availability of diverse data integrated into a common framework is expected to be of high value not only for basic studies on lectin biology but also in in pursuing several applications in biotechnology, immunology and clinical practice, using these molecules.
Available links for the lectin database:
- Plant Lectin Database
- Cancer Lectin Database
- Animal Lectin Database
- Bacterial Lectin Database
- Fungal Lectin Database
 Structural bioinformatics
Core algorithim - compares a pair of binding sites. [ http://proline.physics.iisc.ernet.in/pocketmatch/]
Implements an algorithm for finding binding site (pockets) in protein structures. Can be accessed here.
Detection of hydrogen-bond signature patterns in protein families:
- (a) Detection of hydrogen-bond signature patterns in a family of structures,
- (b) Determination of common hydrogen-bond interactions in a pair of structures
- (c) Calculation of the percentage of conservation for each pair
- (d) Determination of the role of a given amino acid in a conserved interaction
- (e) Correlation with the sequence conservation
The tool can be accessed here.
Determination of Ligand Recognition sites in Protein structures: The list of proteins to which a ligand binds is used to generate a pattern of binding residues of proteins. This pattern will be useful in understanding the residues playing a key role in protein-ligand interaction. The types of interactions determined using this tool are polar, van der Waal's and covalent interactions. The tool can be accessed here.
 Systems biology
 Pathway Analyser
PathwayAnalyser (PA) is a tool for systems biologists for analysis of metabolic pathways, particularly by Flux Balance Analysis and ODE simulation. PA interfaces with the GNU Linear Programming Toolkit (GLPK) for linear programming, as well as with Taylor for performing high precision simulations (e.g. using GMP). It can give a comprehensive report on gene deletions from the Systems Biology Markup Language (SBML) Model input. It is written in C++ and uses libSBML and GLPK. PA is meant for linux (excl. cygwin at the moment) but it is planned that it will be usable in all platforms. More details can be found on the PathwayAnalyser Project Page.
 Genetic Algorithm for studying T-cell recognition
More information soon...