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Vaidehi, Nagarajan, Ph.D. Bookmark and Share

Laboratory of Nagarajan Vaidehi, Ph.D.

Lab Members:
 
Supriyo Bhattacharya, Ph.D.
Postdoctoral Fellow
sbhattach@coh.org

Vamshi Gangupomu, Ph.D.
Postdoctoral Fellow
vgangupomu@coh.org
 
Hubert Li
Graduate Student
huli@coh.org
 
Allen Mao
System Administrator
amao@coh.org
 
Michael Matthew
Summer Student, UC San Diego
 
Daniela Mueller
Postdoctoral Fellow
dmueller@coh.org
 
Michiel Niesen
Research Associate
mniesen@coh.org
 
In-Hee Park
Postdoctoral Fellow
ipark@coh.org
 
Past Lab Members:
 
Spencer Hall, Ph.D.
Army Research Lab
 
Jianping Lin, Ph.D.
Professor Nanjai University, China
 
Gouthaman Balaraman, Ph.D.
Systems Analyst
 
Alfonso Lam, Ph.D.
Postdoctoral Fellow U.C. Irvine
 
Kyle Roberts
Graduate Student Duke University
 
Bram Van Hoof
Graduate Student TuE eindhoven, Netherlands
 
Michael Debertrand
Dutch Royal Navy
 
Keven Patel
Lehigh University
 

Nagarajan Vaidehi, Ph.D. Research

Proteins are allosteric nano-machines whose conformational dynamics controls their functional versatility. Conformational dynamics is important in understanding the allosteric nature of proteins, in identifying allosteric druggable sites as well as in designing drugs with functional specificity.
 
Biophysical experimental methods provide fragmented information on the structure and dynamics and the X-ray crystallography provides a static picture of one of the low energy conformations in an ensemble of states. Therefore computational methods are essential in integrating the experimental information and provide an atomic level detail of the dynamics of proteins. One of the major bottlenecks in using the existing computational methods to study dynamics of proteins is the limitation in time scale and the narrow conformational search afforded by these methods. Thus we need multi-scale computational methods that span a larger range in time and length scale to extend the use of computational methods to large protein complexes. Our laboratory is focused on developing state of the art multi-scale computational methods to study the conformational dynamics of proteins. We are developing coarse grain computational methods to sample the various kinetic states of the protein dynamics, followed by fine grain computational methods to capture the detailed atomic level structural changes and to calculate the thermodynamic properties.
 
Our research projects include:
 
  1. Development of constrained molecular dynamics methods – GNEIMO
  2. Development of coarse grained conformational sampling method for G-protein coupled receptors (GPCRs) – GPCRSimKit
  3. Development of computational method for designing thermostable mutants for GPCRs – LITiConDesign
  4. Development and application of computational methods to identify allosteric sites for drug design in protein-protein complexes – AlloBindSite
  5. Application of these methods to design drugs with functional specificity for GPCRs targeting pancreatic cancer and other cancers – Chemokine
 

Vaidehi, Nagarajan, Ph.D.

Laboratory of Nagarajan Vaidehi, Ph.D.

Lab Members:
 
Supriyo Bhattacharya, Ph.D.
Postdoctoral Fellow
sbhattach@coh.org

Vamshi Gangupomu, Ph.D.
Postdoctoral Fellow
vgangupomu@coh.org
 
Hubert Li
Graduate Student
huli@coh.org
 
Allen Mao
System Administrator
amao@coh.org
 
Michael Matthew
Summer Student, UC San Diego
 
Daniela Mueller
Postdoctoral Fellow
dmueller@coh.org
 
Michiel Niesen
Research Associate
mniesen@coh.org
 
In-Hee Park
Postdoctoral Fellow
ipark@coh.org
 
Past Lab Members:
 
Spencer Hall, Ph.D.
Army Research Lab
 
Jianping Lin, Ph.D.
Professor Nanjai University, China
 
Gouthaman Balaraman, Ph.D.
Systems Analyst
 
Alfonso Lam, Ph.D.
Postdoctoral Fellow U.C. Irvine
 
Kyle Roberts
Graduate Student Duke University
 
Bram Van Hoof
Graduate Student TuE eindhoven, Netherlands
 
Michael Debertrand
Dutch Royal Navy
 
Keven Patel
Lehigh University
 

Research

Nagarajan Vaidehi, Ph.D. Research

Proteins are allosteric nano-machines whose conformational dynamics controls their functional versatility. Conformational dynamics is important in understanding the allosteric nature of proteins, in identifying allosteric druggable sites as well as in designing drugs with functional specificity.
 
Biophysical experimental methods provide fragmented information on the structure and dynamics and the X-ray crystallography provides a static picture of one of the low energy conformations in an ensemble of states. Therefore computational methods are essential in integrating the experimental information and provide an atomic level detail of the dynamics of proteins. One of the major bottlenecks in using the existing computational methods to study dynamics of proteins is the limitation in time scale and the narrow conformational search afforded by these methods. Thus we need multi-scale computational methods that span a larger range in time and length scale to extend the use of computational methods to large protein complexes. Our laboratory is focused on developing state of the art multi-scale computational methods to study the conformational dynamics of proteins. We are developing coarse grain computational methods to sample the various kinetic states of the protein dynamics, followed by fine grain computational methods to capture the detailed atomic level structural changes and to calculate the thermodynamic properties.
 
Our research projects include:
 
  1. Development of constrained molecular dynamics methods – GNEIMO
  2. Development of coarse grained conformational sampling method for G-protein coupled receptors (GPCRs) – GPCRSimKit
  3. Development of computational method for designing thermostable mutants for GPCRs – LITiConDesign
  4. Development and application of computational methods to identify allosteric sites for drug design in protein-protein complexes – AlloBindSite
  5. Application of these methods to design drugs with functional specificity for GPCRs targeting pancreatic cancer and other cancers – Chemokine
 
Our Scientists

Our research laboratories are led by the best and brightest minds in scientific research.
 

Beckman Research Institute of City of Hope is internationally  recognized for its innovative biomedical research.
City of Hope is one of only 41 Comprehensive Cancer Centers in the country, the highest designation awarded by the National Cancer Institute to institutions that lead the way in cancer research, treatment, prevention and professional education.
Learn more about City of Hope's institutional distinctions, breakthrough innovations and collaborations.
Develop new therapies, diagnostics and preventions in the fight against cancer and other life-threatening diseases.
 
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By giving to City of Hope, you support breakthrough discoveries in laboratory research that translate into lifesaving treatments for patients with cancer and other serious diseases.
 
 
 
 
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