tag:blogger.com,1999:blog-7844526396210378482.post1070152191900942808..comments2024-01-31T09:23:26.925+00:00Comments on Noel O'Blog: Introducing Webel - A cheminformatics toolkit built solely on webservicesNoel O'Boylehttp://www.blogger.com/profile/03288289351940689018noreply@blogger.comBlogger6125tag:blogger.com,1999:blog-7844526396210378482.post-50507793283721868332009-11-10T16:37:31.709+00:002009-11-10T16:37:31.709+00:00Just realised that your name isn't mentioned, ...Just realised that your name isn't mentioned, Markus. I've corrected that omission.Noel O'Boylehttps://www.blogger.com/profile/03288289351940689018noreply@blogger.comtag:blogger.com,1999:blog-7844526396210378482.post-18985931933013699572009-11-10T16:32:55.157+00:002009-11-10T16:32:55.157+00:00Hi Noel, as I wrote to you by email I really like ...Hi Noel, as I wrote to you by email I really like the idea of Webel - nice work!<br /><br />@nyc_dad: As Noel wrote: at the very backend the Chemical Structure Resolver uses Cactvs which deals with stereochemistry very carefully.<br />However, if you encounter any problems please report them to usMarkus Sitzmannhttps://www.blogger.com/profile/09375886130230910119noreply@blogger.comtag:blogger.com,1999:blog-7844526396210378482.post-56640696093024279472009-11-05T19:57:31.853+00:002009-11-05T19:57:31.853+00:00Thanks for the encouragement Sargis! I think you w...Thanks for the encouragement Sargis! I think you will need access to the core CDK API to do what you want, so the Cinfony cdk module is the way to go. I intend to write a similar blog post on using this.Noel O'Boylehttps://www.blogger.com/profile/03288289351940689018noreply@blogger.comtag:blogger.com,1999:blog-7844526396210378482.post-70205495684858889772009-11-05T18:35:14.091+00:002009-11-05T18:35:14.091+00:00Nice work! After reading about Cinfony, I was hesi...<b>Nice work!</b> After reading about Cinfony, I was hesitating to use it, but this new module (Webel) seems to be what I needed. In particular, <br />I want to align some molecules and I came across <a href="http://openbabel.org/wiki/Obfit" rel="nofollow">Obfit</a> that seems to require SMARTS pattern provided by the user. What I need is a method that would not require this input and Kabsch alignment implemented in CDK and described in <a href="http://chem-bla-ics.blogspot.com/2009/11/new-bioclipse-features-kabsch-alignment.html" rel="nofollow">chem-bla-ics Blog</a> seems to be what I need. I'll see if I can do this with Webel. <b>Keep up the good work!</b>Sargishttps://www.blogger.com/profile/01730048467387998912noreply@blogger.comtag:blogger.com,1999:blog-7844526396210378482.post-41092112129534102922009-11-05T16:39:14.088+00:002009-11-05T16:39:14.088+00:00The underlying data model is a SMILES string. This...The underlying data model is a SMILES string. This is capable of storing cis/trans and tetrahedral stereochemistry. So the question then is, do the webservices honor stereochemistry? In the case of the CDK webservices, there is no problem as stereochemistry doesn't affect the results (e.g. the molecular weight). In the case of the NCI services, stereochemistry appears to be preserved (you can try a chiral SMILES-->InChI-->SMILES roundtrip to test this).Noel O'Boylehttps://www.blogger.com/profile/03288289351940689018noreply@blogger.comtag:blogger.com,1999:blog-7844526396210378482.post-78902117457911734732009-11-05T16:25:46.998+00:002009-11-05T16:25:46.998+00:00Does this handle stereochemistry?Does this handle stereochemistry?nyc dadhttps://www.blogger.com/profile/12408630866156325938noreply@blogger.com