Publications

The original paper describing SEED is the following:

• 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.

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

The accurate energy continuum electrostatic model implemented in SEED was introduced in:

• M. Scarsi, J. Apostolakis, and A. Caflisch.

  Continuum Electrostatic Energies of Macromolecules in Aqueous Solutions.

  J. Phys. Chem. A, 101 (43): 8098–8106, 1997.

  doi: 10.1021/jp9714227

The fast energy model is described in the second SEED paper:

• N. Majeux, M. Scarsi, and A. Caflisch.

  Efficient electrostatic solvation model for protein-fragment docking.

  Proteins: Structure, Function and Genetics, 42:256-268, 2001.

  doi: 10.1002/1097-0134(20010201)42:2<256::AID-PROT130>3.0.CO;2-4

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.

  doi: 10.1016/j.ejmech.2018.07.042

Recent 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.

  J. Chem. Inf. Model., 60(10):4881–4893, 2020.

  doi: 10.1021/acs.jcim.0c00556