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Cell2Chem Implementation

The Cell2Chem was implemented using MySQL database engine and Django web framework, while all the scripts were written in Python. JSME[1] and RDKit[2] were used for input and visualization of molecular structure.

 


 

Query related biosynthetic compounds by species (chassis cells)

 

Search options

1561794903665

You can retrieve the biosynthetic compounds you are interested in by scientific or generic name of the species.

 


 

Query related species(chassis cells) by compound

 

Search options

1561794871075

You can retrieve species (chassis cell) you are interested in by means of text, SMILES, fragment, similarity, maximum common substructure (MCS).

 

1561801385752

It is also possible to use a compound image based retrieval method implemented by JSME.

 


 

Query compounds by DNA sequence

 

Search options

1561804106346

You can upload fasta files containing DNA sequences to retrieve compounds in enzyme-catalyzed reactions encoded by this sequence, based on the BrEPS[3] protocol.

 


 

Query relevant DNA sequences by compound

 

Search options

1561804900686

You can retrieve the DNA sequence that codes for the enzyme involved in the reaction by compound's SMILES.

 

1561801385752

It is also possible to use a compound image based retrieval method implemented by JSME.

 

 

FAQ

 

References

  1. B Bienfait, P Ertl. JSME: a free molecule editor in JavaScript. Journal of cheminformatics. 2013;5:24.doi:10.1186/1758-2946-5-24
  2. SA Rahman, G Torrance, L Baldacci, S Martinez Cuesta, F Fenninger, N Gopal, S Choudhary, JW May, GL Holliday, C Steinbeck, JM Thornton. Reaction Decoder Tool (RDT): extracting features from chemical reactions. Bioinformatics. 2016;32(13):2065-6.doi:10.1093/bioinformatics/btw096
  3. Dudek et al.: BrEPS 2.0: Optimization of sequence pattern prediction for enzyme annotation. PLOS ONE 2017 12(7)