Kathryn Armstrong

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32 Vassar Street, Room 32-211
Cambridge, MA 02139
kathryn AT mit DOT edu



My graduate research is in the area of computational methods for structure-based molecular design.

I work on development and application of computational methods for structure-based molecular design and analysis. Specifically, I use protein sequence and structure search methods to study molecular diversity and accelerated evolution techniques, I have used information theory to analyze multiple sequence alignments, and I have used electrostatic calculations to study proteins and small molecules.

More details about my thesis research.


  • Biological Kinetics and Cellular Dynamics. In the Spring of 2006 I was an instructor for this undergraduate course taught by professors Douglas Lauffenburger and Forest White. I taught students to use MATLAB to numerically solve systems of ordinary differential equations and to do curve fitting and parameter estimation.
  • For one month in the summer of 2001 I helped teach a computer-networking course at the University of Science and Technology in Kumasi, Ghana through the Technology for Education Program.


  • K. A. Armstrong, B. Tidor, and A C. Cheng “Optimal charges in lead progression: A structure-based Neuraminidase case study” J. Med. Chem. 2006 Apr 20; 49 (8): 2470-7. abstract
  • O. Sakarya*, K. A. Armstrong*, M. Adamska, M. Adamski, B. M. King, I. F. Wang, D. Sachdu, B. Tidor, B. Degnan, T. Oakley, K. S. Kosik “A Post-synaptic Scaffold at the Origin of the Animal Kingdom” Submitted to Nature. (*equal contributors)


  • Biophysical Society Annual Meeting, Long Beach, CA, USA. February 2005.
  • CSAIL Student Workshop, Gloucester, MA, USA. September 2005.
  • Bioengineering and Toxicology Seminar, MIT, Cambridge, MA, USA. February and October 2005.
  • DuPont-MIT Alliance Symposium, Cambridge, MA, USA. Annual updates, 2003-2006.
  • AIChE SBE First International Conference on Biomolecular Engineering, Coronado Island, CA, USA. January 2007.

Other research

  • In the summer of 2004 I did an internship at the Pfizer Research Technology Center, working with Dr. Alan Cheng in the Molecular Informatics group. We studied the Neuraminidase active site and its interaction with several therapeutic drugs and published a paper showing that charge optimization techniques can aid in lead-optimization of drugs for this influenza virus enzyme.
  • I did undergraduate research in Professor Michael Klein's lab: the Center for Molecular Modeling at the University of Pennsylvania. As part of my work I coded and parallelized the Fast Multipole Method algorithm for molecular dynamics simulations and learned about molecular dynamics algorithms.
  • In the summer of 2001 I worked in the Computational Biology research group at the IBM Almaden Research Center. Mentored by Dr. William Swope, Dr. Julia Rice, and Dr. Jed Pitera I studied TIP and SPC water models by analyzing molecular dynamics simulations. I wrote scripts to test various properties of water models such as density and enthalpy of vaporization as well as hydrogen-bond kinetics. I also implemented a parallelized replica-exchange method (using Metropolis scheme) for molecular dynamics.