Alan Chen

  • Alan Chen


    Dr. Chen’s laboratory focuses on the use of molecular simulations to computationally predict the 3- D structure and function of RNA. Our approach focuses on using “virtual experiments” that facilitate interpretation of biophysical experiments and produce testable predictions. In past work, we have also used simulations to explain the enhanced mechanical stability of a minimal 2-bp “kissing-loop” involved in MMLV retrovirus dimerization, and explained the observed cation-specificity of model RNA kissing-loop complex. We have also recalibrated the underlying physical parameters used to simulate RNA to match thermodynamic experiments; this resulted in the first published report of de-novo folding of a non-canonical RNA motif to sub- angstrom resolution. We are currently applying this technology to decipher the structural-thermodynamic “rules” that govern RNA-loop driven molecular recognition processes in RNA viruses, such as the IRES- ribosome interactions in Cricket Paralysis Virus, the dimerization initiation site in HIV, and miRNA binding to Hepatitis C.