.. _publications:

Publications 
============

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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.
  | :raw-html:`<a class="reference external" href="http://dx.doi.org/doi:10.1002/(SICI)1097-0134(19991001)37:1<88::AID-PROT9>3.0.CO;2-O">doi: 10.1002/(SICI)1097-0134(19991001)37:1<88::AID-PROT9>3.0.CO;2-O</a>`

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.
  | :raw-html:`<a class="reference external" href="http://dx.doi.org/doi:10.1021/jp9714227">doi: 10.1021/jp9714227</a>`

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.
  | :raw-html:`<a class="reference external" href="http://dx.doi.org/doi:10.1002/1097-0134(20010201)42:2<256::AID-PROT130>3.0.CO;2-4">doi: 10.1002/1097-0134(20010201)42:2<256::AID-PROT130>3.0.CO;2-4</a>`
  
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.
  | :raw-html:`<a class="reference external" href="http://dx.doi.org/doi:10.1016/j.ejmech.2018.07.042">doi: 10.1016/j.ejmech.2018.07.042</a>`

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.
  | :raw-html:`<a class="reference external" href="https://doi.org/10.1021/acs.jcim.0c00556">doi: 10.1021/acs.jcim.0c00556</a>`