[OTDev] LogP modeling challenge
Nina Jeliazkova jeliazkova.nina at gmail.comWed Feb 23 13:05:54 CET 2011
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On 23 February 2011 14:02, Martin Guetlein <martin.guetlein at googlemail.com>wrote: > On Wed, Feb 23, 2011 at 10:53 AM, Nina Jeliazkova > <jeliazkova.nina at gmail.com> wrote: > > Hello All, > > > > In an exercise to reproduce an ECOSAR model, I've found the current > > implementation of XLogP (CDK ) performs a bit different compared to > KOWWIN > > [1]. > > > > http://tinyurl.com/xlogp-kowwin > > Hi Nina, > > I am not a CDK expert, but I just recently noticed that it contains > two methods for LogP calculation. > Have but have you tried the ALOGPDescriptor method (instead of > XLOGPDescriptor) as well? > > ALogP is so much worse that I didn't dare to send the comparison chart to a public list :) http://apps.ideaconsult.net:8080/ambit2/chart/xy?dataset_uri=http://apps.ideaconsult.net%3A8080%2Fambit2%2Fdataset%2F186293&feature_uris[]=http%3A%2F%2Fapps.ideaconsult.net%3A8080%2Fambit2%2Ffeature%2F430904&feature_uris[]=http://apps.ideaconsult.net:8080/ambit2/feature/114589 Nina Regards, > Martin > > > > > This makes hard to reproduce the ECOSAR model, since it depends on LogP. > > Also, LogP is an important parameter in many toxicity prediction models. > > > > This is why, I think it is an opportunity for everybody within OpenTox > (and > > outside) to create a better LogP prediction model from a dataset, which > has > > been recently made available to OpenTox . Models would be built > preferably > > via OpenTox API , but not necessary (in that case we could consider > wrapping > > the models into OpenTox API later) . > > > > Models can be then validated by OpenTox validation service at > ALU-Freiburg > > and best one(s) selected. > > > > The dataset is available via OpenTox dataset service (several formats via > > HTTP Accept:mime-type header ) > > > > http://apps.ideaconsult.net:8080/ambit2/dataset/181563 > > http://apps.ideaconsult.net:8080/ambit2/dataset/181563 > > > > (minimal) metadata > > http://apps.ideaconsult.net:8080/ambit2/dataset/181563/metadata > > > > The target feature (experimental LogKow value) is at > > http://apps.ideaconsult.net:8080/ambit2/feature/430867 ) > > > > Would be nice to have a validated OpenTox LogP model (or more than one!) > . > > > > Best regards, > > Nina > > > > [1] http://www.epa.gov/opptintr/exposure/pubs/episuite.htm > > _______________________________________________ > > Development mailing list > > Development at opentox.org > > http://www.opentox.org/mailman/listinfo/development > > > > > > -- > Dipl-Inf. Martin Gütlein > Phone: > +49 (0)761 203 8442 (office) > +49 (0)177 623 9499 (mobile) > Email: > guetlein at informatik.uni-freiburg.de >
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