Biomanufacturing Workbench of BIONODE

Dive into our Biomanufacturing Workbench, a powerful suite within BIONODE designed to link natural products (NPs) with genomic data and accelerate bio‑based product development. Whether you’re mining bacterial genomes, exploring fungal pathways, or matching small molecules to their genetic origins, these tools give you everything you need in one user‑friendly platform.

1. antiSMASH

• Identify and characterize biosynthetic gene clusters (BGCs) from sequence files (GenBank, EMBL, or FASTA). Beyond basic detection, antiSMASH offers:
• KnownClusterBlast & SubClusterBlast: Compare your BGCs with curated databases
• MIBiG Comparison: Link clusters to experimentally validated NPs
• Pfam & TIGRFam Analysis: Annotate with protein families and GO terms
• TFBS & ActiveSiteFinder: Predict regulatory elements and enzyme active sites
• RREFinder: Detect ribosomally synthesized and post‑translationally modified peptide clusters
• Your results include BGC identifiers, cluster types, NP details, predicted functions, and sequence coordinates—ready for downstream analysis.

2. fungiSMASH

• Tailored for fungal genomes, fungiSMASH refines candidate BGC boundaries using expert‑curated models. Simply upload your GenBank,
• EMBL, or FASTA file to:
• Optimize cluster predictions based on protein domains and functional motifs
• Annotate fungal-specific NP pathways
• Generate high‑confidence candidate lists for natural product discovery

3. Chemsearch

• Map small molecules back to their genomic producers. Provide a compound structure or COCONUT_DB ID (e.g., CNP0190579), and Chemsearch will:
• Preprocess reaction and fingerprint data (using RDKit)
• Filter and match against genomic databases
• Return genomes likely to produce your query molecule
• Highlight taxonomy and biosynthetic potential for experimental follow‑up
• This end‑to‑end workflow supports everything from target identification to therapeutic or agricultural product development.
• Version 1.0—and growing. We’re continuously expanding these tools to empower your next breakthrough in bio‑product discovery.