Changes between Version 2 and Version 3 of DDBJ-KEGG-PDBj

Timestamp:

2009/03/17 17:25:09 (16 years ago)

Author:

akinjo

Comment:

--

DDBJ-KEGG-PDBj

@@ -6 +6 @@
 Finding pathway components (enzymes) that are expected to form physical contacts as judged from homologous protein structures.
 
+In short, find the physical protein-protein interaction networks of homologous pathways in various species.
+
 == The procedure ==
 
-1. Pick a pathway of a specific organism, say Glycolysis / Gluconeogenesis pathway of Homo sapiens (human).
-1. Get all the amino acid sequences of that pathway component.
-1. Run blast for each sequence against UniProt(SwissProt / TrEMBL).
-1. Group the blast results according to biological species (s1, s2, ..., sn).
- 
+=== Part I ===
+ 1. Pick a pathway of a specific organism, say Glycolysis / Gluconeogenesis pathway of Homo sapiens (human).
+ 1. Get all the amino acid sequences of that pathway component (c''1'', c''2'', ..., c''m'').
+=== Part II ===
+ 1. Run blast for each sequence against !UniProt(!SwissProt / TrEMBL).
+ 1. Group the blast results according to biological species (s''1'', s''2'', ..., s''n'').
+ 1. For each pathway component (c''i''), pick the top hit from each species.
+  *  At this step, you have (at most) an ''m'' compoents X ''n'' species array of protein sequences: '''Homologous Compoenents Matrix''' (HCM).
+=== Part III ===
+ 1. Pick one column (species) of the HCM (s''j'') For each component of that column, run blast against PDB sequences.
+  * You will have a list of PDBID and Chain ID as a result of this blast search.
+ 1. If the blast results of two components share the same PDB ID but do not share the same Chain ID, they are judged to be in contact.
+  * By regarding each pathway component as a node,  the inferred physical contacts between two components correspond to an edge in the network.
+ 1. Iterate the above two steps for each column of the HCM.
+ 1. Finally, show the list of inferred PPI of the pathway for each species.
+