|Software and Databases|
Current Focus: Systems biology application to understanding diseases, immunological processes. An obvious outcome will be an application of the obtained knowledge in drug and vaccine discovery.
Development of Virtual mycobacterial cell models and their analysis to
- Address mechanism of drug action.
- Identify most appropriate drug targets.
- Study carbohydrate recognition in pathogenesis.
- Carbohydrate recognition and immunological triggers
The present focus in the laboratory different areas towards deriving appropriate system landscapes at different levels of hierarchy and different levels of model abstraction, and build mathematical models to simulate them. Such models will then be used to address
- (a) role of recognition of carbohydrates in tuberculosis pathogenesis
- (b) consequences of carbohydrate recognition in triggering specific immune mechanisms relevant to tuberculosis,
- (c) identify appropriate drug targets for tuberculosis and
- (d) study the pharmacodynamic profiles of the existing anti-mycobacterial drugs.
Work has already been initiated in this direction by building a first level virtual cell of the mycobacterium. A model of this system is built using a systems biology modelling toolkit. A new algorithm that encodes advanced bioinformatics tools and methods, is under development, to define the minimum system model for a given purpose. As proof-of-concept, a simulation of the system defined for H2-antihistamines has been carried out, which reveals the paradoxical accumulation of histamine available for binding by H1-receptor, upon using H2-antihistamines, thus explaining their adverse effects.
A long-term goal in the laboratory is to derive general principles and sub-system ontologies, their representation and incorporation into tractable models, so as to enable disease modelling.
Genome and proteome sequence analysis: Mycobacterium tuberculosis
- Identification of pathways, Identification of function for several proteins, comparative genomics, Identification and feasibility analysis of drug targets
- Metabolic Pathway Analysis, Flux Balance Analysis, Identification of newer drug targets based on flux analyses, Identification of protein–protein influences based on metabolic pathway participation
- Algorithms for detecting signature interaction patterns in protein structures
- Study of Determinants of molecular recognition
- Analysis of fold and function determinants
- Development of an integrated lectin knowledge base, its usage in analysis of lectins, identification of potential applications of lectins in clinical practice, biotechnology and agriculture
- Cancer-lectin database
Protein structure determination by X-ray crystallography
Crystal structures of:
- Garlic lectin
- RecA protein
- Phosphoglycerate kinase
- Structural genomics of proteins from Mycobacterium tuberculosis
- Towards Rational Vaccine design: In silico identification of CTL epitopes from Mycobacterium tuberculosis – Implications to Vaccine design
- Elucidating mechanisms of drug action
- Structure-based drug design (lead identification, protein-ligand interactions)
- Structure prediction, Molecular modelling and Fold recognition
- Structure of the globular domain and C-terminal domains of the rat linker histone
- Structure of the chromatosome particle