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 homolgous 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 COMPOUND
Protein Sequence ID
(UniProt:ID/AC, RefSeq:protein_id)
(ADRB1_HUMAN,NP_000675.1)
Amino acid sequence:

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

Upload your PDB file:

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

SMILES string:

CC(NCC(COc1cccc3nc2ccccc2c31)O)C

Upload your 3D compound file:

SDF MOL MOL2 PDB

Draw a query compound by JSME editor

CAUTION: an uploading compound file should have a 3D conformation with proper bond lengthes and angles. A planar 2D structure is not good for 3D modeling.


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.
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