Research & Development

Overview

Our work focuses on the application of theory, computer models, and informatics to noncovalent binding and molecular recognition. We are particularly interested in developing software and data resources that will be of value in understanding these phenomena and in designing molecules that bind to specific targets. We also use isothermal titration calorimetry to measure host-guest binding thermodynamics, and use these data to test computational models of binding.

Research Areas (updated May 2014)

  • Calculation and characterization of changes in entropy and enthalpy in molecular recognition.
  • Preorganization and entropy-enthalpy compensation
  • Application of molecular dynamics and liquid state theory to the structure and thermodynamics of water in protein binding sites, and its role in molecular recognition.
  • Calculation of binding free energies: double decoupling, attach-pull-release, etc
  • Computational analysis of mechanical stress at the molecule level
  • Host-guest and supramolecular systems
  • Synthetic polymer-peptide conjugates
  • Organometallic catalysts
  • Force field development
  • Protein kinases, especially protein kinase A
  • Computer-aided drug-design in collaboration with experimental groups
  • BindingDB: a publicly accessible database of measured protein-small molecule affinities