The Vaidehi lab develops physics-based computational methods to study the structure, function and dynamics of proteins and protein complexes. These methods are useful in studying protein-protein interactions and identifying and optimizing small-molecule drugs to inhibit these interactions. Vaidehi’s specific interests are in studying the G-protein-coupled receptor dynamics – as in the interaction of chemokines – and antagonists to the chemokine receptors that trigger leukocyte migration in immune response and inflammation. Prediction of the binding-site interactions of agonists and antagonists with the receptors greatly streamlines the drug development process.
GNEIMO (Generalized Newton-Euler Inverse Mass Operator) is an Internal Coordinate Molecular Dynamics (ICMD) method developed in collaboration with Dr. Abhinandan Jain at the NASA Jet Propulsion Laboratory, Caltech.
The GneimoSim software can be downloaded free of cost for academic use by submitting the request form shown below. Once the form is submitted we will send you a downloadable link to the software.
Allosteer: This software used molecular dynamics trajectories and calculates the network of amino acid residues involved in allosteric communication between two specified sites in a protein. It also calculates the pipeline of this communication and lists all the residues involved in this communication pipeline. To download Allosteer for non-commercial academic use please submit the request form below. Once the form is submitted we will send you a downloadable link to the software.
The Chair of the Department of Computational and Quantitative Medicine, Nagarajan Vaidehi conducts research that focuses on developing physics-based computational methods to study protein structure, dynamics and drug design.
B.Tech., Bioinformatics, Vellore Institute of Technology University, Tamil Nadu, India
Ph.D., Computational Chemistry, University of Georgia
Biased agonism using classical MD simulations, biased ligand design, studying the effects of allosteric communication in GPCRs using MD and AlloSteer, understanding the molecular basis for subtype selectivity and method development.