Reactzyme: A benchmark for enzyme-reaction prediction
Enzymes, with their specific catalyzed reactions, are necessary for all aspects of life,
enabling diverse biological processes and adaptations. Predicting enzyme functions is …
enabling diverse biological processes and adaptations. Predicting enzyme functions is …
Enzymeflow: Generating reaction-specific enzyme catalytic pockets through flow matching and co-evolutionary dynamics
Enzyme design is a critical area in biotechnology, with applications ranging from drug
development to synthetic biology. Traditional methods for enzyme function prediction or …
development to synthetic biology. Traditional methods for enzyme function prediction or …
Training on test proteins improves fitness, structure, and function prediction
Data scarcity and distribution shifts often hinder the ability of machine learning models to
generalize when applied to proteins and other biological data. Self-supervised pre-training …
generalize when applied to proteins and other biological data. Self-supervised pre-training …
Reaction-conditioned De Novo Enzyme Design with GENzyme
The introduction of models like RFDiffusionAA, AlphaFold3, AlphaProteo, and Chai1 has
revolutionized protein structure modeling and interaction prediction, primarily from a binding …
revolutionized protein structure modeling and interaction prediction, primarily from a binding …
EnzymeCAGE: A Geometric Foundation Model for Enzyme Retrieval with Evolutionary Insights
Enzyme catalysis is fundamental to life, driving the chemical transformations that sustain
biological processes and support industrial applications. However, unraveling the …
biological processes and support industrial applications. However, unraveling the …
Sequence-based TCR-Peptide Representations Using Cross-Epitope Contrastive Fine-tuning of Protein Language Models
Understanding T-Cell receptor (TCR) and epitope interactions is critical for advancing our
knowledge of the human immune system. Traditional approaches that use sequence …
knowledge of the human immune system. Traditional approaches that use sequence …
FGW-CLIP: Enhancing Enzyme Screening via Fused Gromov-Wasserstein Contrastive Learning
Enzymes are crucial catalysts for biochemical reactions, underpinning numerous biological
processes. The efficient identification of specific enzymes from extensive protein libraries is …
processes. The efficient identification of specific enzymes from extensive protein libraries is …