Further Information

Other applications using Browndye

  • Simulation-Enabled Estimation of Kinetic Rates (SEEKR).


Here are some images from scientific projects using Browndye.

A sample successful trajectory, showing that the ligand explores significant space before finding the binding site. This sample NA contains glycans from the Glyprot server. Sialic acid (not to scale) is superimposed on the left side of the image for clarity. Seitz et. al. Biophysical Journal, 119, 2275-2289, 2020.

Barnase-barstar complex (1BRS) sample trajectory (R. Konecny/Pymol).

Christian Seitz / unpublished

Christian Seitz / unpublished

Votapka, Lane W., and Rommie E. Amaro. "Multiscale estimation of binding kinetics using brownian dynamics, molecular dynamics and milestoning." PLoS Comput Biol 11.10 (2015): e1004381.

Votapka, Lane W., et al. "SEEKR: simulation enabled estimation of kinetic rates, a computational tool to estimate molecular kinetics and its application to trypsin–benzamidine binding." The Journal of Physical Chemistry B 121.15 (2017): 3597-3606.

Amaro, Rommie E., et al. "A computational assay that explores the hemagglutinin/neuraminidase functional balance reveals the neuraminidase secondary site as a novel anti-influenza target." ACS central science 4.11 (2018): 1570-1577.


An example of unsuccessful and sucessful (binding event) trajectory (C. Seitz).