Model Heat Shock 90 Protein
URMI ROY
urmi@clarkson.edu

 

 

 

 

 

 

 

 

 

 

 

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Protein Modeling and Protein Chemistry
Protein Dynamics and Protein Simulations


Research Interests

My current research interest is in the field of Structural Biology, and I am particularly interested in Protein Chemistry and Protein Modeling. My research focuses mostly on the molecular interactions between ligands and receptors, and I am interested in exploring their applications for innovative drug discovery. The specific aspects of my ongoing research are:

  • Modeling of Receptor Proteins
  • Protein-Peptide/Protein-Protein Docking
  • Identification of Ligand-Receptor Interactions at the Interface
  • Solvation Effect (Explicit Solvation and Molecular Dynamics Simulation)
  • Protein-Protein Interaction (PPI): Identification of Potential Receptor Protein using PPI Network
  • Educational Protein Modeling for Undergraduates

Tumor Differentiation Factor (TDF) and its Potential Receptor Protein

A
B

C

A. Ribbon diagram of human heat shock 70kDa protein 9. B. Schematic diagram showing the ligand (ATP) - receptor (78 kDa glucose-regulated protein) interactions in 3LDL (Chain A). The pink circles represent the residues participating in hydrogen bonds, as well as in charge or polar interactions. The green circles are residues participating in van der Waals interactions. The light blue circle surrounding a given residue/atom denotes the latter's solvent accessible surface. The main chain and side-chain hydrogen bonds are indicated by green and blue dashed arrows. H-bond with water is depicted in black arrow. Pi interaction and charge interactions are colored in orange and pink dashed line respectively. Water molecules are displayed as cyan sphere. C. Molecular Dynamics simulation of solvated TDF protein (water molecules are not displayed).


Protein-Protein Interaction
(Proteomics and Structure based Bioinformatics Approaches)


Estrogen Receptor
Educational Protein Modeling for Undergraduates
Estrogen Receptor with backbone and sidechain

vdw contact

1usi
1usk_A

Peptide Chemistry and Thiol Protection