Dan Kirshner

Contact information

Lawrence Livermore National Laboratory
7000 East Avenue, L-367
Livermore, CA 94550
email: kirshner1@llnl.gov
phone: 925 422 4802


University of California, Santa Cruz, B.A. Physics, 1976
University of California, Santa Cruz, B.A. Economics, 1976


I conduct research in computational biology.  I work on protein function prediction, particularly prediction of catalytic function (see the Catalytic Site Identifcation web server) and on prediction of catalytic reaction rates from data produced by molecular dynamics simulations.  In a past life I was an economic analyst for an environmental organization.

Selected publications

Timothy S. Carpenter, Daniel A. Kirshner, Edmond Y. Lau, Sergio E. Wong, Jerome P. Nilmeier, and Felice C. Lightstone (2014).  A Method to Predict Blood-Brain Barrier Permeability of Drug-like Compounds Using Molecular Dynamics Simulations.  Biophys. J. (2014) 107(3), 630-641.

D. A. Kirshner, J. P. Nilmeier, and F. C. Lightstone (2013).  Catalytic Site Identification – A Web Server to Identify Catalytic Site Structural Matches Throughout PDB. Nucleic Acids Research, 41, W256-W265

J. P. Nilmeier, D. A. Kirshner, S. E. Wong, and F. C. Lightstone (2013).  Rapid Catalytic Template Searching as an Enzyme Function Prediction ProcedurePLoS ONE, 8(5), e62535.

James J. Langham, Ann E. Cleves, Russell Spitzer, Daniel Kirshner, Ajay N. Jain (2009).   Physical Binding Pocket Induction for Affinity Prediction. Journal of Medicinal Chemistry.

Jake Gunn Glanville, Dan Kirshner, Nandini Krishnamurthy, and Kimmen Sjolander (2007).  Berkeley Phylogenomics Group Web Servers: Resources for structural phylogenomic analysis. Nucleic Acids Research; doi:10.1093/nar/gkm325.

Nandini Krishnamurthy, Duncan Brown, Dan Kirshner and Kimmen Sjölander (2006).  PhyloFacts: An online structural phylogenomic encyclopedia for protein functional and structural classification.  Genome Biology, 7:R83.

Daniel Kirshner (2001), Efficiency Gains From Value Pricing: Case Study of Sunol Grade” Transportation Research Record, No. 1747.

Daniel Kirshner, Barbara Barkovich, Kathy Treleven, and Robin Walther (1997).  A Cost-effective Renewables Policy Can Advance the Transition to Competition, The Electricity Journal, Vol. 10, No. 1.

Daniel Kirshner and Deborah Moore (1989).  The Effect of San Francisco Bay Water Quality on Adjacent Property Values. Journal of Environmental Management, 27.

Daniel Kirshner (1984).  Statistical Tests of Energy Savings Due to Voltage Reduction.  Institute of Electrical and Electronics Engineers Transactions, Vol. PAS‑103.

Daniel Kirshner (1980).  Some Non-explanations of Bicycle Stability, American Journal of Physics.

Daniel McFadden, Carlos Puig, and Daniel Kirshner (1979).  Determinants of the Long-Run Demand for Electricity.  Journal of the American Statistical Association.