Dear Jmol People, I've implemented a novel method for evaluating conserved protein features from databases such as CDD using JSmol. You can check it out here:
http://bar.utoronto.ca/CDD3D The user submits a query protein sequence of interest to search for similar proteins from the RCSB or homology model databases. Selecting a related structure will populate JSmol (or Jmol if you choose) and if there are CDD features they will be mapped to the structure. To evaluate conservation, there are interactive alignments as HTML text that communicate directly with the structure model using Javascript. You can try for example this sequence: SVWRAINKQTGEVVAIKKMKKKYYSWDECINLREVKSLRRMNHPNIVKLKEVIRENDILYFVFEYMECNLYQLMKDRQKLFAEADIKNWCFQVFQGLSYMHQRGYFHRDLKPENLLVSKDIIKIADFGLAREVNSSPPFTEYVSTRWYRAPEVLLQSYVYTSKVDMWAMGAIMAELLSLRPIFPGASEADEIYKICSVIGTPTEETWLEGLNLANTINYQFPQLPGVPLSSLMPSASEDAINLIERLCSWDPSSRPTAAEVLQHPFFQSCFYVPPSLRPKPSVARTPPPVGPRGSFEHQSVKRYPVSLANAKPFNSYVSPKSNAAFGSGVQRKLDMVNQDGTRNTKPVRSSVRDSKYRPPGKKSPHNAAAASLNKNRVTRSSVSETADKLANMTIGATGSRRHSVSVVGQHQQLKPPPMKAGWVGETRDMFLRPTQ I'd be very happy to receive feedback! Perhaps you can help me with a problem - in JSmol the context menu is obscured for some reason that I can't figure out... probably something to do with the layout/CSS. Any help in this respect would be very much appreciated! Thank you all very much for your fantastic work on Jmol/JSmol. ~Geoff -- Geoffrey Fucile, PhD Université de Genève Département de Biologie Moléculaire Sciences III 30 quai Ernest-Ansermet CH-1211 Genève 4 ------------------------------------------------------------------------------ Introducing Performance Central, a new site from SourceForge and AppDynamics. Performance Central is your source for news, insights, analysis and resources for efficient Application Performance Management. Visit us today! http://pubads.g.doubleclick.net/gampad/clk?id=48897511&iu=/4140/ostg.clktrk _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
