SMARTCyp News

May 21st 2013. Version 2.4.2 has been released featuring:
Bug fix: reading of some sdf files did not work properly

March 22nd 2013. Version 2.4.1 has been released featuring:
Update of the ChemDoodle web components library to version 5.1
Bug fix: Improved aromaticity detection in HTML output.
Bug fix: Corrected aromatic SMILES output from the filter function.

January 16th 2013. Version 2.4 has been released featuring:
Inclusion of solvent accessible surface area (SASA) in the scoring function.
SASA is computed using the 2DSASA algorithm from 2D coordinates.

November 5th 2012. Version 2.3 has been released featuring:
Improved energies for N-oxidations
Empirical correction for unlikely N-oxidations of tertiary alkylamines
A filtering functionality for excluding compounds with very low activation barriers to CYP-mediated oxidations
A smiles string can now be input directly on the command line using the -smiles flag.
Details on the new usage on the download page

May 30th 2012. Version 2.2 has been released featuring:
One new energy rule for sulfur atoms double bonded to sp2 carbon atoms.
Update protonated amine SMARTS matching due to analysis of larger 2D6 data set.
Faster predictions by rewriting our SMARTS matching code for the pharmacophores in the 2D6 and 2C9 models.
Web site update with links to the 2C9 model paper, and prediction accuracy results on nine different isoforms.

May 9th 2012. Version 2.1.1 has been released featuring:
Bug fix to the html display, top rank label rings were wrong in 2.1.

May 1st 2012. Version 2.1 has been released featuring:
Specific prediction of CYP2C9 mediated drug metabolism.
Improved reactivity for several functional groups.
A paper describing the 2C9 model has been published: P. Rydberg and L. Olsen "Predicting Drug Metabolism by Cytochrome P450 2C9 - Comparison to the 2D6 and 3A4 Isoforms"" ChemMedChem, 2012, DOI: 10.1002/cmdc.201200160.

March 14th 2012. Version 2.0.3 has been released featuring:
A new command line flag (-outputfile) has been added due to a user request.

March 12th 2012. Version 2.0.2 has been released featuring:
A fix to the HTML output which did not draw rank circles around all symmetric atoms with the new ChemDoodle HTML.

January 25rd 2012. Version 2.0.1 has been released featuring:

• The 2D sketcher is now the one from ChemDoodle, which makes the website compatible with mobile phones and touch screen tablets.
• The HTML output from SMARTCyp will now by default give HTML5 canvas figures using ChemDoodle Web Components. This makes SMARTCyp roughly ten times faster in generating HTML output.
• This new output is supported by all new web browsers, however it requires internet access when viewing the output (to fetch the ChemDoodle javascript libraries from our server).
• The old HTML output with PNG images can still be generated using a new flag, -png, which was added to the command line program.

November 1st 2011. Version 2.0 has been released featuring:
Specific prediction of CYP2D6 mediated drug metabolism.
Improved reactivity for benzothiophene sulfurs.
A paper describing the 2D6 model has been published: P. Rydberg and L. Olsen "Ligand-based Site of Metabolism Prediction for Cytochrome P450 2D6" ACS Medicinal Chemistry Letters, 2012, 3, 69-73.

November 29th 2010. Update to the web site:
A paper describing the SMARTCyp web server has been published: P. Rydberg, D.E. Gloriam, L. Olsen "The SMARTCyp cytochrome P450 metabolism prediction server" Bioinformatics, 2010, 26, 2988-2999
Updates of web pages related to the results in the paper.

October 21st 2010. Version 1.5.3 has been released featuring:
Additional -printall command line option to print all non-hydrogen atoms to csv output.

August 23rd 2010. Version 1.5.2 has been released featuring:
Improved Internet Explorer 8 support in HTML output.
Improved handling of input files with errors in them.

August 23rd 2010. Web server and general news:
The stability of the server when incompatible files are uploaded have been improved.
SMARTCyp is now also available as modules for ToxTree (included by default), and Pipeline Pilot (download available).


July 1st 2010. Version 1.5 has been released including the following improvements and functionalities:

General for SMARTCyp:

• Improved performance due to better SMARTS rules based on 72 new DFT calculations.
• Highlighting of top 3 ranked atoms.
• Improved symmetry perception.

Java program:

• Options for suppressing HTML or CSV output.
• Option for directing output to a specific directory.

SMARTCyp is a service from the Department of Drug Design and Pharmacology at the University of Copenhagen, funded by Lhasa Limited.