Predict protein function by docking

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Step 1. get a protein of unknown function

http://kb.psi-structuralgenomics.org/kb/search.do?type=unkstruc

Step 2. use DOCK Blaster to predict what binds

(see John for latest instructions

  • use pocket picker to pick pockets
  • find any ligands in ZINC that may be close (based on similarity/alignment below)
  • leads and fragments

1. use http://blaster3.docking.org/ (use the pocket picker feature)

Step 3. while docking is running, perform additional research

  • sequence similarity
  • fold analysis and classification

Step 4. Find out if someone can test for binding (contact original structural genomics center)

  • probably best to do this after you have plausible looking ligands

Step 5. order compounds

Step 6. test for binding