tag:blogger.com,1999:blog-7844526396210378482.post1154711958725720299..comments2024-01-31T09:23:26.925+00:00Comments on Noel O'Blog: 4th Joint Sheffield Conference on ChemoinformaticsNoel O'Boylehttp://www.blogger.com/profile/03288289351940689018noreply@blogger.comBlogger8125tag:blogger.com,1999:blog-7844526396210378482.post-23649732736202582222009-08-29T05:52:47.696+01:002009-08-29T05:52:47.696+01:00"Docking Tools need cross validation and a es..."Docking Tools need cross validation and a essential set of input parameters concerned with the job assigned." i have used GOLD and many others and found what u offer to calculate using a statistical method should be compatible under limitations using the extreme of it...<br />Ultimately its u who decides the way you want to work a software...Mukesh Yadavnoreply@blogger.comtag:blogger.com,1999:blog-7844526396210378482.post-75462247067535677572007-07-14T08:27:00.000+01:002007-07-14T08:27:00.000+01:00" I don't think people realise that all docking pr..." I don't think people realise that all docking programs perform well on some targets and not so well on others (and it's different for each program)."<BR/><BR/>You should also add that it is not possible in advance to tell which program will work best for which target.<BR/><BR/>Also for targets with known ligands it would be interesting to see how the docking/scoring tools compare with the use of simple 2D descriptors.chrishttps://www.blogger.com/profile/06616449115962971854noreply@blogger.comtag:blogger.com,1999:blog-7844526396210378482.post-51710953307945571772007-06-23T00:03:00.000+01:002007-06-23T00:03:00.000+01:00Two PhD students from my former institute have tak...Two PhD students from my former institute have taken the JOELib2 responsibility, but it might take a while for them to get productive. They told me that they have done already some GUI and mining extensions, but those things are still internal (I guess for publishing reasons).<BR/><BR/>As said, I am completely busy with my PostDoc and my job at Tibotec. Extending JOELib2 is not an active part of it, not at the moment. And I think this status will not change for a while, because I have higher priorities elsewhere. And, as usual, I am working on them very seriously.Anonymoushttps://www.blogger.com/profile/09112376168632883058noreply@blogger.comtag:blogger.com,1999:blog-7844526396210378482.post-43798423171387565532007-06-22T23:50:00.000+01:002007-06-22T23:50:00.000+01:00Beside the things mentioned already, David highlig...Beside the things mentioned already, <A HREF="http://davidjwild.googlepages.com/home" REL="nofollow">David</A> highlighted also <A HREF="http://cheminfo.informatics.indiana.edu/~rguha/" REL="nofollow"> Rajarshi's</A> and <A HREF="http://chem-bla-ics.blogspot.com/" REL="nofollow">Egon's</A> support to the Web2.0 things presented.<BR/><BR/>And there was a critical and eligible question of <A HREF="http://www.eyesopen.com/about/staff/bios.html#ant" REL="nofollow">Anthony Nicholls</A> why this is done? The problem is that no company will ever submit molecular structures into the WWW, because this is just not safe and violates intellectual property protection. There he is abolutely right and he was also the one freaking out the whole docking community by giving a brilliant and refreshing talk.<BR/><BR/>David answered that education is the main goal and the next time anyone asks, we should not forget that setting standards is another goal. And, companies can always use intranet solutions on the same technology. So, there is indeed a reason for working on Web2.0 technologies. And especially 'the problem' of companies is the reason why universities should work on this. As already said by David might those mixtures lead to very innovative ways looking at data.Anonymoushttps://www.blogger.com/profile/09112376168632883058noreply@blogger.comtag:blogger.com,1999:blog-7844526396210378482.post-70255672779868116092007-06-22T16:13:00.000+01:002007-06-22T16:13:00.000+01:00@james: Great, thanks for clarifying that@egon: I ...@james: Great, thanks for clarifying that<BR/><BR/>@egon: I don't think people realise that all docking programs perform well on some targets and not so well on others (and it's different for each program). What does 'prediction error' mean in this context, though? Anthony Nicholls wants to improve the average AUC of a ROC curve across all targets. I think this is reasonable. However, even then, since the AUC of a ROC curve is simply directly related to the average rank of an active (as derived in the <A HREF="http://dx.doi.org/10.1021/ci600426e" REL="nofollow">BEDROC paper</A>), maybe the AUC value itself already hides some useful information, i.e. which is better, to predict some actives in the top 1% and some in the bottom 1%, or all actives in the centre around 50%.<BR/><BR/>I spoke briefly with Joerg about Joelib2, and other things. I think at the moment he is busy getting to grips with his new job.Noel O'Boylehttps://www.blogger.com/profile/03288289351940689018noreply@blogger.comtag:blogger.com,1999:blog-7844526396210378482.post-70510208769547789342007-06-22T16:04:00.000+01:002007-06-22T16:04:00.000+01:00Sorry, forgot to add the DOI for that paper: 10.10...Sorry, forgot to add the DOI for that paper: 10.1021/ci050282s.Egon Willighagenhttps://www.blogger.com/profile/07470952136305035540noreply@blogger.comtag:blogger.com,1999:blog-7844526396210378482.post-46533323430213467832007-06-22T16:00:00.000+01:002007-06-22T16:00:00.000+01:00In reply to the comments on docking. Last time I s...In reply to the comments on docking. Last time I saw plots at the German Chemoinformatics Conference I was amazed by the prediction errors, and am happy that more people think that too :) I also found in my own research that those error bars apply to many QSAR and QSPR studies (see ). Below 100 objects you can forget purely statistic validation to give reasonable results. The error margin on, for example, R^2/Q^2 is in the order of 0.05. Any model which is does not have a R^2 or Q^2 more than 0.05 better, is not significant. The more objects in your data set, the smaller this error margin (obviously).<BR/>(BTW, I only learned about ROC curves about a year ago... too late for my research; it seems really useful.)<BR/><BR/>Thanx for the links to the other statistics. Sounds interesting.<BR/><BR/>Good to see further adoption of opensource here too. Did you talk with Joerg about the state of JOELib2?Egon Willighagenhttps://www.blogger.com/profile/07470952136305035540noreply@blogger.comtag:blogger.com,1999:blog-7844526396210378482.post-40386416002714449552007-06-22T15:09:00.000+01:002007-06-22T15:09:00.000+01:00Re: the Nottingham code using JOELib2. The TMACC c...Re: the Nottingham code using JOELib2. The TMACC code is available under the GPL, just like JOELib. I've updated the webpage and the README to explicitly state the licence. Cheers.Unknownhttps://www.blogger.com/profile/16580073343180585571noreply@blogger.com