Structural Bioinformatics

Structural Bioinformatics

A major focus of the team is to adopt innovative strategies to identify modulators of interfaces in protein-protein interactions (PPIs). High-throughput interaction discovery initiatives have revealed the existence of hundreds of multi-protein complexes whose functions are regulated through thousands of PPIs. However, the structural details of these dynamic interactions are limited. Computational methodologies involving simulation of biological macromolecules are employed by the team to scrutinize PPI interfaces. The aim here is to scan for the spatial arrangement of hot-spot residues, or the existence of any binding clefts or extended regions in the interaction domains. Such analysis is subsequently employed for the generation of small synthetic modulators that either promote or inhibit a given protein-protein interaction.

Additionally, the team also drives the early translational activities at DDRC. To this end they develop and apply experimentally driven in silico modeling methods for the discovery of bioactive molecules (hits). To assess protein dynamics, molecular recognition at atomic level resolution is employed.

Such approaches also enable study of various physically and biologically important questions like allostery, identification of allosteric drug binding sites, ligand driven conformational changes in proteins, biological functions emerging from structure, drug resistance, and inhibition mechanisms. Working then in collaboration with the medicinal chemistry and biological assay teams, the hits derived from such exercises are optimized into leads.

Infrastructure

  • Cluster Setup for parallel computing
  • High end workstations and server setup
  • GPU Cluster
  • Analysis tools like Schrodinger, VMD, Amber etc

The Team

  • Shailendra Asthana (PhD), Scientist C
  • Charu Suri (PhD), Research Associate
  • Mitul Srivastava (MSc), Senior Research Fellow
  • Mritunjay Singh (M.Pharm), Senior Research Fellow
  • Anita Kumari (M.Pharm), Junior Research Fellow
  • Lovika Mittal (M.Tech, Junior Research Fellow