NP.searcher takes in DNA sequence and outputs the Simplified Molecular Input Line Entry Specifications (SMILES) of the predicted possible polyketide and nonribosomal peptide natural products from the DNA sequence. If an entire genome is input, all the recognized clusters and their possible products are output.
1. Upload DNA sequence in FASTA format by clicking the 'Browse..." button and the location of the FASTA file.
2. Select the molecular weight range of sought molecules or leave as default.
3a. Check or leave as default check boxes for displaying unknown units. If checked, instead of showing closest predicted substrate, the output will be a generic peptide or ketide. This may not be interpreted by many chemical software.
3b. Choose or leave as default automatic heterocyclization. Though this may find heterocyclized moieties in the form of oxazole or thiazole groups, it will also increase the number of predicted molecules. You may also perform automatic glycosylation, but not both, since the possibilties increase too much to be practical.
4. Submit job.
5. Wait for job to run. Large genomes may take a few minutes while clusters may finish within a minute.
6. Once complete, click on link to cluster of interest.
7. Copy and paste SMILES string into ChemDraw or other software that can convert SMILES to 2D or 3D structure.