Skip to content

UnixJunkie/SEED-mirror

Repository files navigation

SEED (Solvation Energy for Exhaustive Docking) version 4.0.0

SEED is a program for fragment docking with force-field based evaluation of binding energy.

The new SEED documentation is now online at: https://caflischlab-seed.readthedocs.io/en/latest/!

For details about the energy models implemented in SEED please refer to the original publications and to the pdf user manual (seed_4.0.0_doc.pdf).

Installation

cd to directory src and make SEED with the following command (you may have to modify the Makefile.local):

make seed

The binary is compiled into the bin directory.

Run SEED

Run SEED with the following command:

./seed_4 seed.inp >& log

You can find an example seed.inp and seed.par, along with the results of simple study cases, in the test_cases folder.

Citations

Assessment of SEED on 15 different protein targets, with a focus on its scoring power. Advantages, limitations and practical tips for usage are discussed:

  • K. Goossens, B. Wroblowski, C. Langini, H. van Vlijmen, A. Caflisch, and H. De Winter. Assessment of the Fragment Docking Program SEED. Journal of Chemical Information and Modeling, 60(10):4881–4893, 2020.
    https://doi.org/10.1021/acs.jcim.0c00556

Review of the applications of SEED in the period 1999-2018, including a discussion on its strenghts and weaknesses in light of our experience:

Original paper describing SEED:

Second SEED paper including the description of the fast energy evaluation:

Accurate energy continuum electrostatic model implemented in SEED:

  • M. Scarsi, J. Apostolakis, and A. Caflisch. Continuum Electrostatic Energies of Macromolecules in Aqueous Solutions. The Journal of Physical Chemistry A, 101(43):8098–8106, 1997.
    https://doi.org/10.1021/jp9714227