SEED - Solvation Energy for Exhaustive Docking¶
SEED is a program for fragment docking with force-field based evaluation of
binding energy.
The implemented docking approach determines optimal positions and orientations
of small-to-medium-sized molecular fragments in the binding site
of a rigid receptor, and ranks them according to their binding energy.
Polar fragments are positioned such that at least one hydrogen bond with
optimal distance to a protein polar group is made (polar docking).
Apolar fragments are docked by matching hydrophobic regions on the
fragment and on the receptor (apolar docking).
These regions are efficiently and accurately determined
by evaluating electrostatic desolvation penalty and van der Waals
interactions with an uncharged probe sphere.
Two implicit solvation models based on the Generalized Born methodology
are employed to efficiently evaluate the protein and fragment desolvation
upon binding and the screened electrostatic interaction.
NEW! The best generated poses can now be minimized in rigid-body spaces with Monte Carlo Simulated Annealing and/or Steepest Descent. Beware that these new features are experimental and have not been tested thoroughly yet.
NEW! A new keyword-based parameter file has been introduced. This allows more flexibility in
the way settings are specified, but only involves newly added parameters
(e.g. the ones for Monte Carlo Simulated Annealing or Steepest Descent),
so that legacy seed.par files keep working as expected. See Keyword-based parameter file for details.
SEED is developed in the Caflisch Lab at the University of Zurich and hosted on GitLab under the GNU General Public License version 3 (GPLv3).
If you use SEED in your work, please cite the original SEED paper:
- N. Majeux, M. Scarsi, J. Apostolakis, C. Ehrhardt, and A. Caflisch. Exhaustive docking of molecular fragments on protein binding sites with electrostatic solvation. Proteins: Structure, Function and Genetics, 37:88-105, 1999.
Go to Publications for an overview of articles related to SEED.