EC-BLAST

[…] biologically incorrect predictions (i.e., subsequent reaction steps may use different stereoisomers). however, stereochemical changes have already been captured by many computational tools such as ec-blast and reaction decoder tool , which use the chemistry development kit (cdk) , and clca to model stereochemical changes by appending stereochemical descriptors to the canonical labeling […]

[…] based not on amino acid sequence similarity but on chemical structure similarity. several other methods to predict ec numbers from chemical structures have been subsequently developed [–], including ec-blast [], which allows one to search for enzymatic reactions with ec numbers that are similar to the query reaction based on bond-change, reaction-center, or reaction-structure similarity., enzyme […]

[…] attributes from biochemical reactions such as bond changes is necessary to compare enzymes based on the chemistry of their catalysed reactions. in order to calculate chemical attributes we used ec-blast, a recently-developed algorithm to obtain accurate atom-atom mapping, extract bond changes and perform similarity searches between enzyme reactions []., to study reaction diversity across […]

[…] within the same fold group., though the ec numbering system is good for curating enzyme functions, it is not useful for making quantitative comparisons between reaction chemistries. by using ec-blast, we can quantify the functional changes observed in the ec exchange matrix by calculating similarities in bond order changes, reaction centres, and substrate/product sub-structures (). […]

[…] are comparatively analysed using functional and all-against-all sequence similarity., to explore the evolution of the isomerases, we have calculated the functional similarity between enzymes using ec-blast [], a recently developed algorithm to automatically compare biochemical reactions. this approach introduces three measures of functional similarity — comparison of bond changes, reaction […]