Click on the "Choose File" button to upload a TSV file:

The data uplaoded to this website will be stored for a day and then deleted. If you have protected data, please use the SIMMER tool locally using the instructions here.

Enter information manually:

(All fields are required)

Reaction identifier:   e.g. DM1

  substrate(s)+cofactor(s)   product(s)

Names: e.g. 4-asa


SMILES: e.g. C1=CC(=C(C=C1N)O)C(=O)O.CC(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(C)COP(=O)(O)OP(=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)N2C=NC3=C(N=CN=C32)N)O)OP(=O)(O)O)O


Input help

  • The user can enter any text into the left_comp and right_comp columns (as seen in the DM3 example below), but for the reaction column must identify a query using 'DM' followed by any alphanumeric character (SIMMER distinguishes queries from its database of MetaCyc reactions by 'seeing' the DM label).
  • If the query includes multiple substrates and/or products (as seen in the DM2 example below), their respective SMILES must be separated by a '.'
  • SIMMER can process either canonical or isomeric SMILES; the MetaCyc database uses isomeric SMILES where available.
  • If the user has more than one query, they will want to input their queries as a tsv file organized as follows:
    reaction_identifier substrate_cofactor_name product_name substrate_cofactor_smiles product_smiles
    DM1 brivudine bromovinyluracil OC[C@H]1O[C@H](C[C@@H]1O)N1C=C(\C=C\Br)C(=O)NC1=O Br\C=C\C1=CNC(=O)NC1=O
    DM2 gemcitabine 2′, 2′-difluorodeoxyuridine NC1=NC(=O)N(C=C1)[C@@H]1O[C@H](CO)[C@@H](O)C1(F)F.O.[H+] OC[C@H]1O[C@@H](N2C=CC(=O)NC2=O)C(F)(F)[C@@H]1O.[NH4+]
    DM3 foo bar C1=CC=C2C(=C1)C(=NO2)CS(=O)(=O)N O=C(CS(=O)(N)=O)C1=CC=CC=C1O