[Dock-fans] need your help!
yustar2003 at 126.com
Thu Apr 14 00:16:11 PDT 2005
I am a beginner in using DOCK program. I met some difficulties in my research and need your help. I am currently doing my dissertation on the vaccine design, one very important step is to make sure the epitope (ligand) match well with the MHC molecular. I learn that the prerequisite for using the DOCK is having the coordinates or the pdb file of both epitope and MHC molecular. My problem is that I have no structural information of epitope, only have the primary sequence. Since most molecular modeling program need the length of input sequence no shorter than 25~30 residues, while epitope for MHC class I is about 10 mer length and 10~15 mer for MHC class II, so I feel puzzled what shall I do now. Can you do me a favor and give me some suggestions? Thank you!
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