HOMCOS:Modeling Protein-Compound Complex

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This service generates a 3D model of protein-compound complex for a given query protein sequence and query compound, using a homologous protein complex 3D structure as a template. A query amino acid sequeuce is input by UniProt ID, one letters amino acid sequence, [PDB_ID]+[Chain Identifier] or uploading your PDB file, . A query compound can be input by three ways: input 3-letter compound code of PDB, input a SMILES string, or uploading chemical coumpound file (in SDF, MOL, MOL2 or PDB).

Protein Sequence ID
(UniProt:ID/AC, RefSeq:protein_id)
Amino acid sequence:

PDB_ID:(2rh1, 1fin, 4hhb,...) CHAIN_ID:(A, B, ...)

Upload your PDB file:

3-letter compound code of PDB(recommeneded):
(CAU, ATP, G39,A1LU6,...)

KEGG compound/drug code(recommended):
(D07608, D00002, D01977...)

Upload your 3D compound structure file (recommended):


SMILES string(2D;not recommended):


Draw a query compound by JSME editor (2D;not recommended)

CAUTION: an uploading compound file should have a proper 3D conformation. A planar 2D structure and a SMILES string are not good for correct 3D modeling. We recommended to input PDB 3-letter or KEGG code, or to upload a compound file with 3D structure.

Parameters for BLAST sequence search

Parameters for KCOMBU chemical structure search

The sequence search is performed by BLAST. The chemical compound search is performed by KCOMBU.
Comments and Questions to :

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