[Dock-fans] About obtaining good sphere cluster!

Zheng elevenren at yahoo.com.cn
Tue Nov 29 01:15:10 PST 2005


Dear DOCK fans:
   
  Based on the DOCK 4.0 manual, the spheres representing the active site can be generated by DOCK/sphgen or by just using the the positions of atoms from the bound ligand. 
   
  I tried to docking a ligand to its receptor protein using both these methods. 
   
  By the former, I couldn¡¯t obtain good docking result (by compare to the complex NMR structure) when considering the flexibility of ligands.
   
  While by the latter, I got much better docking result than the former. But because we just have one complex NMR structure, we can¡¯t use another ligand to validate these spheres.
   
  Then how to get the good sphere cluster, which can better reproduce the complex NMR structure and is without the bias of the known ligand binding mode?
   
  Every advice is appreciated!
   
   
  P.S. Does anyone have the detailed manual of the CLUSTER------the accessory software of DOCK?
   


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        ***************************************
        *          Zheng Canhui               *
        *                                     *
      _ *         Pharmacy School             * _
     / )* Second Military Medical University  *( \
    / / *         Shanghai, China             * \ \
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