Journal
NUCLEIC ACIDS RESEARCH
Volume 45, Issue W1, Pages W49-W54Publisher
OXFORD UNIV PRESS
DOI: 10.1093/nar/gkx320
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Funding
- National Science and Engineering Research Council [RGPIN 371576-2009, 101997-2006, 388681-2011]
- Canada Research Chair (CIHR) New Investigator Award
- Ontario Early Investigator Award
- Canada Research Chairs Program
- CIHR Operating Grant
- CIHR-Joint Programming Initiative on Antimicrobial Resistance Research Grant
- Canadian Institutes of Health Research
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Microbial natural products represent a rich resource of pharmaceutically and industrially important compounds. Genome sequencing has revealed that the majority of natural products remain undiscovered, and computational methods to connect biosynthetic gene clusters to their corresponding natural products therefore have the potential to revitalize natural product discovery. Previously, we described PRediction Informatics for Secondary Metabolomes (PRISM), a combinatorial approach to chemical structure prediction for genetically encoded nonribosomal peptides and type I and II polyketides. Here, we present a ground-up rewrite of the PRISM structure prediction algorithm to derive prediction of natural products arising from non-modular biosynthetic paradigms. Within this new version, PRISM 3, natural product scaffolds are modeled as chemical graphs, permitting structure prediction for aminocoumarins, antimetabolites, bisindoles and phosphonate natural products, and building upon the addition of ribosomally synthesized and post-translationally modified peptides. Further, with the addition of cluster detection for 11 new cluster types, PRISM 3 expands to detect 22 distinct natural product cluster types. Other major modifications to PRISM include improved sequence input and ORF detection, user-friendliness and output. Distribution of PRISM 3 over a 300-core server grid improves the speed and capacity of the web application. PRISM 3 is available at http://magarveylab.ca/prism/.
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