Hi, I agree with Jules : the CDK may not be the right tool for this. Bioclipse has Jmol support, of course - so at least you could make images of binding sites, but it does not have any site-comparison tools that I know of.
You could ask on Biostar : http://biostar.stackexchange.com/ ? Although I am not very familiar with binding site analysis, I do know in general of approaches that could be taken. You could compare the volume of the binding site; the pattern of ligand-protein bonds; create a pharmacophore, ... It really depends on what information you have, how much computation you want to do, and what tools are available (of course!). gilleain On Tue, Mar 22, 2011 at 1:20 PM, Desmond Lim <limwen...@gmail.com> wrote: > Hi, > > I'm a new user of CDK (just started) and my boss needs me to proteins > with similar bindings to one that we have. I have gone through the CDK > website and can't find any documentation on how to go about doing this. > > I'm using Bioclipse. Can someone point me to the right place to start my > search, an SDK, manual, codes, anything? > > Thanks. > > Desmond > > ------------------------------------------------------------------------------ > Enable your software for Intel(R) Active Management Technology to meet the > growing manageability and security demands of your customers. Businesses > are taking advantage of Intel(R) vPro (TM) technology - will your software > be a part of the solution? Download the Intel(R) Manageability Checker > today! http://p.sf.net/sfu/intel-dev2devmar > _______________________________________________ > Cdk-user mailing list > Cdk-user@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/cdk-user > ------------------------------------------------------------------------------ Enable your software for Intel(R) Active Management Technology to meet the growing manageability and security demands of your customers. Businesses are taking advantage of Intel(R) vPro (TM) technology - will your software be a part of the solution? Download the Intel(R) Manageability Checker today! http://p.sf.net/sfu/intel-dev2devmar _______________________________________________ Cdk-user mailing list Cdk-user@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/cdk-user
