Predict protein function by docking: Difference between revisions
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* find any ligands in ZINC that may be close (based on similarity/alignment below) | * find any ligands in ZINC that may be close (based on similarity/alignment below) | ||
* leads and fragments | * leads and fragments | ||
1. use http://blaster3.docking.org/ (use the pocket picker feature) | |||
= Step 3. while docking is running, perform additional research = | = Step 3. while docking is running, perform additional research = | ||
Revision as of 23:06, 12 October 2011
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