Predict protein function by docking: Difference between revisions

From DISI
Jump to navigation Jump to search
No edit summary
 
(3 intermediate revisions by 2 users not shown)
Line 1: Line 1:
=Step 1. get a protein of unknown function =
=Step 1. get a protein of unknown function =
http://kb.psi-structuralgenomics.org/kb/search.do?type=unkstruc
http://kb.psi-structuralgenomics.org/kb/search.do?type=unkstruc
Suggest you actually look at the protein, twirl it around, to check that it is not
a. an alpha helix or similar small fragment
b. DNA or RNA (which will not work with DOCK 3.6, sorry)
c. a single protein of a large complex (e.g. one of the ribosomal Sxx proteins, which has a structure that is not meaningful to interpret via docking.


= Step 2. use DOCK Blaster to predict what binds=
= 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)
1. use http://blaster3.docking.org/    (use the pocket picker feature starting from PDB code or a PDB file (e.g. modbase)
 
2. find actives that are somehow related in some way
 
3. dock biogenic molecules (metabolites, natural products)
 
4. dock drugs - see if any recognized
 
5. dock fragments and/or leads.


= Step 3. while docking is running, perform additional research =
= Step 3. while docking is running, perform additional research =
Line 20: Line 30:


= Step 6. test for binding =
= Step 6. test for binding =
[[Category:Tutorials]]
[[Category:Incomplete]

Latest revision as of 18:02, 15 February 2014

Step 1. get a protein of unknown function

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

Suggest you actually look at the protein, twirl it around, to check that it is not 

a. an alpha helix or similar small fragment
b. DNA or RNA (which will not work with DOCK 3.6, sorry)
c. a single protein of a large complex (e.g. one of the ribosomal Sxx proteins, which has a structure that is not meaningful to interpret via docking.

Step 2. use DOCK Blaster to predict what binds

1. use http://blaster3.docking.org/ (use the pocket picker feature starting from PDB code or a PDB file (e.g. modbase)

2. find actives that are somehow related in some way

3. dock biogenic molecules (metabolites, natural products)

4. dock drugs - see if any recognized

5. dock fragments and/or leads.

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

[[Category:Incomplete]

Retrieved from "http://wiki.docking.org/index.php?title=Predict_protein_function_by_docking&oldid=6174"