---------- Forwarded message ---------- From: Horacio Pérez-Sánchez <horacio@...> Date: Thu, Dec 20, 2012 at 1:03 PM Subject: Re: Molecular flexibility analysis To: Egon Willighagen <[email protected]>
Dear Egon, can the SDK calculate the following fingerprints? FCFP_2, _4, _6 ECFP_2, _4, _6 MDL Public Keys Thanks in advance, Horacio On 24/03/2012, at 10:37, Horacio Pérez-Sánchez wrote: > Dear Egon, > thanks a lot for all the useful information, I have a very good feeling about > the CDK. I will have a look at it later. > Regards, > Horacio > > On 23 Mar , 2012, at 10:51 AM, Egon Willighagen wrote: > >> Dear Horacio, >> >> ---------- Forwarded message ---------- >> From: Horacio Pérez-Sánchez >> Date: 2012/3/23 >> Subject: Molecular flexibility analysis >> >>> I wonder whether Chemistry Development kit tools can be used for, given a >>> database with thousands of ligands, analyzing each ligand and reporting >>> which fragments are rigid and which parts or connetors can be modelled as >>> flexible. >> >> Yes, the CDK can do that. Just as an example, there is a Rotatable >> Bond Count descriptor implemented. >> >> There are various approaches you can take, and it depends a bit on >> what you qualify something as a rigid bond. We have functionality to >> >> - identify ring bonds (SpanningTree class) >> - detect double/triple bonds (simple iteration over all bonds) >> - detect ring systems (we have at least three algorithms to find ring >> systems) >> - classes to do fragmentation, such as the Murcko approach >> >> With kind regards, >> >> Egon >> >> -- >> Dr E.L. Willighagen >> Postdoctoral Researcher >> Department of Bioinformatics - BiGCaT >> Maastricht University (http://www.bigcat.unimaas.nl/) >> Homepage: http://egonw.github.com/ >> LinkedIn: http://se.linkedin.com/in/egonw >> Blog: http://chem-bla-ics.blogspot.com/ >> PubList: http://www.citeulike.org/user/egonw/tag/papers > > ================================================== > Horacio Pérez-Sánchez, PhD > Parallel Computer Architecture Group: http://www.um.es/gacop > School of Computer Science, University of Murcia (Spain) > Email: [email protected] > Tel: + 34 868 88 8509 > ================================================== > ============================================== Horacio Pérez-Sánchez, PhD Parallel Computer Architecture Group: http://www.um.es/gacop School of Computer Science, University of Murcia (Spain) Email: [email protected] Tel: + 34 868 88 8509 ============================================== -- Dr E.L. Willighagen Postdoctoral Researcher Department of Bioinformatics - BiGCaT Maastricht University (http://www.bigcat.unimaas.nl/) Homepage: http://egonw.github.com/ LinkedIn: http://se.linkedin.com/in/egonw Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers ------------------------------------------------------------------------------ LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
