RxnBLAST: molecular scaffold and reactive chemical environment feature extractor for biochemical reactions

MOTIVATION Molecular scaffolds are useful in medicinal chemistry to describe, discuss, and visualize series of chemical compounds, biochemical transformations, and associated biological properties. RESULTS Here, we present RxnBLAST as a web-based tool for analyzing scaffold transformations and reactive chemical environment features in bioreactions. RxnBLAST extracts chemical features from bioreactions including atom-atom mapping, reaction centers, rules, and functional groups to help understand chemical compositions and reaction patterns. Core-to-Core is proposed, which can be utilized in scaffold networks and for constructing a reaction space, as well as providing guidance for subsequent biosynthesis efforts. SUPPLEMENTARY INFORMATION RxnBLAST is available at: http://design.rxnfinder.org/rxnblast/.