Comments on: protonation states and docking http://www.simbiosys.com/blog/2008/05/16/protonation-states-and-docking/ Addressing the challenges of computational drug discovery Thu, 09 Feb 2012 21:38:18 +0000 http://wordpress.org/?v=2.0.11 by: zsolt http://www.simbiosys.com/blog/2008/05/16/protonation-states-and-docking/#comment-1382 Sat, 17 May 2008 16:13:38 +0000 http://www.simbiosys.com/blog/2008/05/16/protonation-states-and-docking/#comment-1382 John, Thanks for making these very useful databases available for the public. We have already used DUD for benchmarking our ligand based screening tool LASSO http://www.simbiosys.ca/ehits_lasso/ , see our publication: LASSO - ligand activity by surface similarity order: a new tool for ligand based virtual screening Journal of Computer-Aided Molecular Design, http://dx.doi.org/10.1007/s10822-007-9164-5, Published online: 18 January 2008, you can access a copy here: http://www.simbiosys.ca/ehits_lasso/lasso_paper_JCAM_2008.pdf We also use referred to it in several conference presentations, e.g.: http://www.simbiosys.ca/science/presentations/2007-pfizer/LASSO-2007_Nov.pdf http://www.simbiosys.ca/science/presentations/echeminfo-2007/LASSO_Wombat_Poster.pdf We will definitely use it to report the results of the new eHiTS version with full protontaion treatment (see next blog post about details). ZZ. John,

Thanks for making these very useful databases available for the public. We have already used DUD for benchmarking our ligand based screening tool LASSO http://www.simbiosys.ca/ehits_lasso/ , see our publication: LASSO - ligand activity by surface similarity order: a new tool for ligand based virtual screening
Journal of Computer-Aided Molecular Design, http://dx.doi.org/10.1007/s10822-007-9164-5,
Published online: 18 January 2008, you can access a copy here:
http://www.simbiosys.ca/ehits_lasso/lasso_paper_JCAM_2008.pdf
We also use referred to it in several conference presentations, e.g.:
http://www.simbiosys.ca/science/presentations/2007-pfizer/LASSO-2007_Nov.pdf
http://www.simbiosys.ca/science/presentations/echeminfo-2007/LASSO_Wombat_Poster.pdf
We will definitely use it to report the results of the new eHiTS version with full protontaion treatment (see next blog post about details).
ZZ.

]]> by: John Irwin http://www.simbiosys.com/blog/2008/05/16/protonation-states-and-docking/#comment-1361 Fri, 16 May 2008 20:51:40 +0000 http://www.simbiosys.com/blog/2008/05/16/protonation-states-and-docking/#comment-1361 I agree. I do hope you will have a chance to report to the community on use use of your algorithm. I would like to volunteer the DUD dataset for this purpose http://dud.docking.org. Kinases are fruitful targets for multiple tautomeric states of aromatic hetrocycles, and metalloenzymes are good targets for testing the effects of deprotonation in the presence of (e.g.) Zn. Both are included in ZINC. I agree. I do hope you will have a chance to report to the community on use use of your algorithm. I would like to volunteer the DUD dataset for this purpose http://dud.docking.org. Kinases are fruitful targets for multiple tautomeric states of aromatic hetrocycles, and metalloenzymes are good targets for testing the effects of deprotonation in the presence of (e.g.) Zn. Both are included in ZINC.

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