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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	COMPOUND
Protein Sequence ID (UniProt:ID/AC, RefSeq:protein_id) (ADRB3_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(recommeneded): (CAU, ATP, G39,A1LU6,...) KEGG compound/drug code(recommended): (D07608, D00002, D01977...) Upload your 3D compound structure file (recommended): SDF MOL MOL2 PDB SMILES string(2D;not recommended): CC(NCC(COc1cccc3nc2ccccc2c31)O)C 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.

• E-value:
  
• min Nresidue_contact_aligned (minNca)
  
• min Ratio of residue_contact_aligned (minRca) (%)
  
• Use precalculated BLAST: (precalc_blt) no yes

• Type of MCS(maximum common substructure):
  Isomorphic Substructure Connected MCS(C-MCS)
  TD-MCS(theta=0) TD-MCS(theta=1) TD-MCS(theta=2)
• Tanimoto similarity:
  0.9 0.8 0.7 0.6 0.6 0.5 0.4 0.2 0.1
  
• Max-number of compound for MCS calculation:
  10 100 500 1000 10000