Close-up of sample being place into microplate

Research Lab Overview

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.

Software

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.

Request form

Learn about our research

Principal Investigator: Nagarajan Vaidehi, Ph.D.

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.

Full bio

Lab Members

Sangbae Lee, Ph.D.

Staff Scientist

B.A., Chemistry, Hanyang University, Seoul, Korea M.S., Physical Chemistry, Hanyang University, Seoul, Korea Ph.D., Physical Chemistry, University of Florida Research interests: Development of biased ligand on angiotensin II type 1 (AT1R) GPCRs Design of novel milder detergent for thermostabilized GPCRs Email: [email protected]

Soumadwip Ghosh, Ph.D.

Postdoctoral Fellow

Education: B.Sc., Chemistry, St. Xavier's College (autonomous) Kolkata, West Bengal, India M.Sc., Applied Chemistry, Indian Institute of Technology Dhanbad, Jharkhand, India Ph.D., Physical Chemistry, Indian Institute of Technology Bombay, Maharashtra, India Research interests: Identifying thermostable point mutations for GPCRs using energy scores and evolutionary constraints, aggregation propensity of chemokine receptors using classical MD simulations. Email: [email protected]

Suvamay Jana, Ph.D.

Postdoctoral Fellow

Education: B.E., Chemical Engineering, Jadavpur University, Kolkata, India M.Tech., Chemical Engineering, Indian Institute of Technology Guwahati, Guwahati, India Ph.D., Chemical Engineering, University of Kentucky, KY, USA. Research interests: To develop and modify computational chemistry tools that can rapidly predict thermostabilizing mutations for membrane receptors, which is a critical step for receptor crystallization Understanding the stability of membrane receptors in various detergent micelles, important for protein extraction and purification.

Ning Ma, Ph.D.

Postdoctoral Fellow

Education: B.S., Biology, Henan Normal University, Xinxiang, China M.S., Microbiology, Huaqiao University, Quanzhou, China Ph.D., Computational Chemistry, University of South Florida, Florida Research interests: Kinase dynamics simulation, GPCR-membrane simulation, conformational free energy simulation, method development. Email: [email protected]

Anita Nivedha, Ph.D.

Postdoctoral Fellow

Education: B.Tech., Bioinformatics, Vellore Institute of Technology University, Tamil Nadu, India Ph.D., Computational Chemistry, University of Georgia Research interests: 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. Email: [email protected]

Sanychen Muk

Research Associate

Education: B.Sc., Bioengineering, University of California, Riverside Research interests: Applying machine learning in the study of GPCR thermostability Email: [email protected]

Philippus Hendrikx

Visiting Scholar

Education: B.Sc., Biomedical Engineering at Eindhoven University of Technology (TU/e) M.Sc., Biomedical Engineering at Eindhoven University of Technology (TU/e) Research interests: Investigating GPCR c-term binding to G-protein through molecular dynamics simulations Email: [email protected]

Shayla Paulekas

Graduate Student

Education: B.A., Biology, University of California, Santa Barbara M.S., Biochemistry, California State University, Northridge Ph.D. (in progress), Biology, Irell & Manella Graduate School of Biological Sciences, City of Hope, Duarte, California Research interests: Studying the molecular mechanisms of partial agonism and allostery in G protein coupled receptors, and how each process influences G protein selectivity3 Email: [email protected]

Manbir Sandhu

Graduate Student

Education: B.S., Human Biology, University of California, San Diego Ph.D., (in progress), Computational Biophysics, Irell & Manella Graduate School of Biological Sciences, City of Hope, Duarte, California Research interests: Delineating the structural features of the GPCR-G protein complex that lead to selective signaling to different G protein pathways Email: [email protected]

Join Our Team

Join one of our labs and help us on our mission to save lives.

Partnerships

Who We Partner With

We collaborate with organizations in progressing the development of new treatments in our specialized areas of research.

NASA Jet Propulsion Laboratory

Boehringer Ingelheim

University of Minnesota

MRC Laboratory of Molecular Biology

Duke University

Stanford University

Support Us

Contribute to our discoveries by donating.

Our Publications

Identifying Functional Hotspot Residues For Biased Ligand Design In G-Protein-Coupled Receptors. Molecular Pharmacology. 2018 Apr 1;93(4):288-96.

Nivedha, A.K., Tautermann, C.S., Bhattacharya, S., Lee, S., Casarosa, P., Kollak, I., Kiechle, T. and Vaidehi, N.

How Does The Proliferating Cell Nuclear Antigen Modulate Binding Specificity To Multiple Partner Proteins? Journal Of Chemical Information And Modeling. 2017 Nov. 57, 12, 3011-3021.

Li, H., Sandhu, M., Malkas, L.H., Hickey, R.J. and Vaidehi, N.

Distinct Structural Mechanisms Determine Substrate Affinity And Kinase Activity Of Protein Kinase Cα. Journal Of Biological Chemistry. 2017 Sep 29;292(39):16300-9.

Lee, S., Devamani, T., Song, H.D., Sandhu, M., Larsen, A., Sommese, R., Jain, A., Vaidehi, N. and Sivaramakrishnan, S.