Publications

A Computational Fragment Approach by Mining the Protein Data Bank: Library Design and Bioisosterism. Moriaud F, Adcock SA, Vorotyntsev A, Doppelt-Azeroual O, Richard SB, Delfaud F. in "Library Design, Search Methods, and Applications of Fragment-Based Drug Design" Editor R.J. Bienstock, Chapter 5, pp 71–88, ACS Symposium Series, Vol. 1076, 2011.
doi: 10.1021/bk-2011-1076.ch005

Identify drug repurposing candidates by mining the Protein Data Bank. Moriaud F, Richard SB, Adcock SA, Chanas-Martin L, Surgand J-S, Ben Jelloul M, Delfaud F. Briefings in Bioinformatics Advance Access published April 21, 2011.
doi: 10.1093/bib/bbr017

Fast and automated functional classification with MED-SuMo: an application on purine-binding proteins. Doppelt-Azeroual O, Delfaud F, Moriaud F, de Brevern AG. Protein Sci. 2010 Apr;19(4):847-67.
PMID: 20162627 Free PMC Article
Free full text

Nucleoside diphosphate kinase and the activation of antiviral phosphonate analogs of nucleotides: binding mode and phosphorylation of tenofovir derivatives. Koch K, Chen Y, Feng JY, Borroto-Esoda K, Deville-Bonne D, Gallois-Montbrun S, Janin J, Moréra S. Nucleosides Nucleotides Nucleic Acids. 2009 Aug;28(8):776-92.
PMID: 20183617

Analysis of HSP90-related folds with MED-SuMo classification approach. Doppelt-Azeroual O, Moriaud F, Delfaud F, de Brevern AG. Drug Des Devel Ther. 2009 Sep 21;3:59-72.
PMID: 19920922 Free PMC Article
Free full text

Computational fragment-based drug design to explore the hydrophobic sub-pocket of the mitotic kinesin Eg5 allosteric binding site. Oguievetskaia K, Martin-Chanas L, Vorotyntsev A, Doppelt-Azeroual O, Brotel X, Adcock SA, de Brevern AG, Delfaud F, Moriaud F. J Comput Aided Mol Des. 2009 Jun 17.
PMID: 19533373

A review of MED-SuMo applications. Doppelt-Azeroual O, Moriaud F, Adcock SA, Delfaud F. Infect Disord Drug Targets. 2009 Jun;9(3):344-57. Review.
PMID: 19519487

Computational fragment-based approach at PDB scale by protein local similarity. Moriaud F, Doppelt-Azeroual O, Martin L, Oguievetskaia K, Koch K, Vorotyntsev A, Adcock SA, Delfaud F. J Chem Inf Model. 2009 Feb;49(2):280-94.
PMID: 19434830

MED-3DMC: a new tool to generate 3D conformation ensembles of small molecules with a Monte Carlo sampling of the conformational space. Sperandio O, Souaille M, Delfaud F, Miteva MA, Villoutreix BO. Eur J Med Chem. 2009 Apr;44(4):1405-9. Epub 2008 Oct 21.
PMID: 19022539

MED-SuMoLig: a new ligand-based screening tool for efficient scaffold hopping. Sperandio O, Andrieu O, Miteva MA, Vo MQ, Souaille M, Delfaud F, Villoutreix BO. J Chem Inf Model. 2007 May-Jun;47(3):1097-110.
PMID: 17477521

Receptor-based computational screening of compound databases: the main docking-scoring engines. Sperandio O, Miteva MA, Delfaud F, Villoutreix BO. Curr Protein Pept Sci. 2006 Oct;7(5):369-93. Review.
PMID: 17073691

The SuMo server: 3D search for protein functional sites. Jambon M, Andrieu O, Combet C, Deléage G, Delfaud F, Geourjon C. Bioinformatics. 2005 Oct 15;21(20):3929-30
PMID: 16141250

A new bioinformatic approach to detect common 3D sites in protein structures. Jambon M, Imberty A, Deléage G, Geourjon C. Proteins. 2003 Aug 1;52(2):137-45.
PMID: 12833538


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