A National Cancer Institute-designated Comprehensive Cancer Center

Make an appointment: 800-826-HOPE

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

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.
 
Support Our Research
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.
 
 
 
 
NEWS & UPDATES
  • Eleven years ago, lymphoma patient Christine Pechera began the long road toward a cancer-free life. She had been diagnosed with non-Hodgkin lymphoma and told by doctors elsewhere that her lifespan likely would be measured in months, not years. Refusing to give up, she came to City of Hope for a second opinion. ...
  • Brain surgery is not for the faint of heart. It takes courage, as well as curiosity and compassion. The truly great surgeons also have a desire to find new, and better ways, of healing the brain. Enter Behnam Badie, M.D., chief of neurosurgery at City of Hope. Now a pioneer in brain tumor treatment, Badie enter...
  • Elizabeth Budde, M.D., Ph.D., wants to encourage infighting. She aims to turn the immune system on itself — to the benefit of patients with acute myeloid leukemia, or AML. AML arises when abnormal white blood cells grow out of control, amassing in the bone marrow and interfering with normal blood cell developme...
  • Six, to date; more soon. Outpatient bone marrow transplants, that is. Finding new ways to deliver quality care with the greatest benefit is a priority for a patient-centered institution like City of Hope. For example, not every bone marrow transplant patient needs to check into the hospital for treatment. In fa...
  • The best measure of success in the fight against cancer is in lives saved and families intact, in extra days made special simply because they exist. Yuman Fong, M.D., chair of the Department of Surgery at City of Hope, understands what precedes that special awareness. When cancer strikes, one minute a person ma...
  • In cancer, expertise matters. So do survival rates, patient safety, patient services and many other factors. City of Hope understands this, as does U.S.News & World Report. The magazine’s 2014-2015 list of best hospitals for cancer once again includes City of Hope, ranking the institution 12 out of 900 elig...
  • At 29, Kommah McDowell was a successful young professional engaged to be married to her best friend. She worked in the financial services sector and kick-boxed to keep in shape and to relax. Then came the diagnosis of triple-negative inflammatory breast cancer, a rare and very aggressive form of breast cancer. ...
  • The well-known drug tamoxifen might not always be the best choice for premenopausal women who have undergone treatment for breast cancer and face a heightened risk of recurrence. A new study suggests that the aromatase inhibitor exemestane, or Aromasin, works slightly better than tamoxifen in preventing cancer ...
  • At age 44, Bridget Hanchette, a mother of three from La Crosse, Wisconsin, was diagnosed with grade IV glioblastoma, the most aggressive type of malignant brain tumor. The cancer grows and spreads quickly, making it difficult to treat. Most patients with this diagnosis are not given much hope, but Hanchette’s i...
  • Survival rates for childhood cancer have improved tremendously over the past few decades, but postcancer care hasn’t always kept up. More children than ever are now coping with long-term complications and side effects caused by their disease and treatment — one of those being learning difficulties. A new ...
  • When Sheldon Querido, a retired manufacturer’s representative, was diagnosed with bladder cancer, his doctor told him that he’d need to have his bladder removed – and that he’d have to wear an external urine-collection bag for the rest of his life. “My first response was ‘I donR...
  • To stop smoking, two approaches might be better than one. A new study has found that using the medication varenicline, or Chantix – along with nicotine patches – was more effective than the medicine alone in helping people quit. The study, conducted by Stellanbosch University in Cape Town, South Africa, and pub...
  • John Cloer was three months shy of his third birthday in 2004 when he was diagnosed with acute lymphoblastic leukemia. For the next three and a half years, he received chemotherapy at City of Hope, finally obtaining long-term remission. His parents Bill and Gina, along with John and his younger brother Steve, r...
  • News about the risks or benefits of widespread cancer screening seem to arrive daily – 3D mammography for breast cancer, CT scans for lung cancer, PSA tests for prostate cancer and now pelvic exams for some women’s cancers. Missing in the headlines is a reflection of how cancer detection is evolving. Today’s ca...
  • Adults with sickle cell disease soon may have a new treatment option: bone marrow transplants. Children with sickle cell disease have been treated successfully with transplantation of bone marrow, more officially known as hematopoietic stem cells, from other people. But the procedure has been less successful in...