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:

• J.-R. Marchand, and A. Caflisch. In silico fragment-based drug design with SEED. European Journal of Medicinal Chemistry, 156:907-917, 2018.
  https://doi.org/10.1016/j.ejmech.2018.07.042

Original paper describing SEED:

• 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.
  https://doi.org/10.1002/(SICI)1097-0134(19991001)37:1<88::AID-PROT9>3.0.CO;2-O

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

• N. Majeux, M. Scarsi, and A. Caflisch. Efficient electrostatic solvation model for protein- fragment docking. Proteins: Structure, Function and Genetics, 42:256-268, 2001.
  https://doi.org/10.1002/1097-0134(20010201)42:2<256::AID-PROT130>3.0.CO;2-4

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