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

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Timestamp:
2009/03/17 17:25:09 (15 years ago)
Author:
akinjo
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  • DDBJ-KEGG-PDBj

    v2 v3  
    66Finding pathway components (enzymes) that are expected to form physical contacts as judged from homologous protein structures. 
    77 
     8In short, find the physical protein-protein interaction networks of homologous pathways in various species. 
     9 
    810== The procedure == 
    911 
    10 1. Pick a pathway of a specific organism, say Glycolysis / Gluconeogenesis pathway of Homo sapiens (human). 
    11 1. Get all the amino acid sequences of that pathway component. 
    12 1. Run blast for each sequence against UniProt(SwissProt / TrEMBL). 
    13 1. Group the blast results according to biological species (s1, s2, ..., sn). 
    14   
     12=== Part I === 
     13 1. Pick a pathway of a specific organism, say Glycolysis / Gluconeogenesis pathway of Homo sapiens (human). 
     14 1. Get all the amino acid sequences of that pathway component (c''1'', c''2'', ..., c''m''). 
     15=== Part II === 
     16 1. Run blast for each sequence against !UniProt(!SwissProt / TrEMBL). 
     17 1. Group the blast results according to biological species (s''1'', s''2'', ..., s''n''). 
     18 1. For each pathway component (c''i''), pick the top hit from each species. 
     19  *  At this step, you have (at most) an ''m'' compoents X ''n'' species array of protein sequences: '''Homologous Compoenents Matrix''' (HCM). 
     20=== Part III === 
     21 1. Pick one column (species) of the HCM (s''j'') For each component of that column, run blast against PDB sequences. 
     22  * You will have a list of PDBID and Chain ID as a result of this blast search. 
     23 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. 
     24  * By regarding each pathway component as a node,  the inferred physical contacts between two components correspond to an edge in the network. 
     25 1. Iterate the above two steps for each column of the HCM. 
     26 1. Finally, show the list of inferred PPI of the pathway for each species. 
     27