RiPPMiner-Genome: A Web Resource for Automated Prediction of Crosslinked Chemical Structures of RiPPs by Genome Mining.
RiPPMiner-Genome is a unique bioinformatics resource for identifying Biosynthetic Gene Clusters (BGC) for RiPPs (Ribosomally Synthesized and Post-translationally Modified Peptides) and automated prediction of crosslinked chemical structures of RiPPs starting from genomic sequences. It is a major update of the RiPPMiner webserver, which used only peptide sequence of RiPP precursors as input for predicting RiPP class and crosslinked chemical structures. Other major improvements are, machine learning (ML) based identification of correct RiPP precursor peptide from among multiple small ORFs (Open Reading Frames) in a BGC, prediction of the cleavage site and cross-links in thiopeptides and identification of non-crosslinked modified residues in lanthipeptides. It has been benchmarked on a dataset of 204 experimentally characterized RiPP BGCs. RiPPMiner-Genome also facilitates visualization of the RiPP BGCs and depiction of the chemical structure of crosslinked RiPP. It also has an interface for searching characterized RiPPs, similar to the predicted core peptide sequence or crosslinked chemical structure.
['Agrawal|Priyesh|P|', 'Amir|Sana|S|', 'Deepak|||', 'Barua|Drishtee|D|', 'Mohanty|Debasisa|D|']
D001331:Automation D001483:Base Sequence D003432:Cross-Linking Reagents D057225:Data Mining D016680:Genome, Bacterial D020407:Internet D017045:Lactococcus D000069550:Machine Learning D010455:Peptides D011499:Protein Processing, Post-Translational D015203:Reproducibility of Results D012270:Ribosomes D012984:Software
RiPP genome mining machine learning cross-link chemical structure prediction