Mehdi D. Davari

This paper elucidates the catalytic mechanism of a PAPS-independent ASST using crystallography and QM/MM simulations, revealing a two-histidine mechanism for sulfo transfer.

This study investigates the substrate specificity and catalytic mechanism of a PAPS-independent ASST from Salmonella typhimurium using structural and computational methods.

SilkRoute provides a reproducible framework for constructing multi-source biomolecular datasets through descriptor-driven workflows.

The paper evaluates how data preprocessing steps affect protein function prediction performance using antioxidant protein classification.

The paper introduces SelectZyme, a platform using protein language models and dimensionality reduction to visualize and explore protein sequence space for enzyme discovery, enabling candidate selection without relying on sequence identity or annotations.

This paper explores integrating explainable AI techniques into machine learning models for predicting protein properties, demonstrating their effectiveness in identifying DNA binding proteins and optimizing Green Fluorescent Protein brightness.

Peptipedia v2.0 expands its peptide database by 45% and integrates machine learning models to annotate peptide sequences with biological activities.

This paper introduces a hybrid model that combines evolutionary probability and machine learning to improve protein engineering with limited data.