4 papers
Rethinking Benchmarks and Models for Enzyme Specificity Prediction
Elizabeth H. Mahood, Natália KomornÃková, Tomáš Pluskal +1
Artificial Intelligence has had a profound impact on the biological sciences, and in particular has accelerated research on protein form and function. Enzymes are no exception: a s…
MassSpecGym in the Wild: Uncovering and Correcting Evaluation Pitfalls in AI-Driven Molecule Discovery
Hongxuan Liu, Roman Bushuiev, Ivy Lightheart +12
Reliable benchmarking is critical for developing machine learning models for tandem mass spectrometry (MS/MS) based molecule discovery. Subtle issues in experimental design and mod…
One protein is all you need
Anton Bushuiev, Roman Bushuiev, Olga Pimenova +9
Generalization beyond training data remains a central challenge in machine learning for biology. A common way to enhance generalization is self-supervised pre-training on large dat…
De novo generation of functional terpene synthases using TpsGPT
Hamsini Ramanathan, Roman Bushuiev, Matouš Soldát +5
Terpene synthases (TPS) are a key family of enzymes responsible for generating the diverse terpene scaffolds that underpin many natural products, including front-line anticancer dr…