Benjamin J. Lengerich

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The positioning of catalytic groups within proteins plays an important role in enzyme catalysis, and here we investigate the positioning of the general base in the enzyme ketosteroid isomerase (KSI). The oxygen atoms of Asp38, the general base in KSI, were previously shown to be involved in anion-aromatic interactions with two neighboring Phe residues. Here(More)
The predictive power of neural networks often costs model interpretability. Several techniques have been developed for explaining model outputs in terms of input features; however, it is difficult to translate such interpretations into actionable insight. Here, we propose a framework to analyze predictions in terms of the model’s internal features by(More)
Methods for retrofitting representations learned from distributional data to the structure of a knowledge graph typically assume that entities are embedded in a connected space and that relations imply similarity. However, knowledge graphs containing diverse entities and relations often do not accord with these assumptions. To overcome these limitations, we(More)
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