António J. M. Ribeiro

The paper develops a geometric matching method to detect catalytic features in protein structures, showing it is more sensitive than sequence-based approaches for identifying homology between distantly related enzymes.

The paper identifies 38 cases of enzymes with different structures but identical functions, analyzing their sequence, structure, and mechanism to support convergent evolution.

EzMechanism automatically generates catalytic mechanism proposals for enzymes by applying biocatalytic rules, validated against 56 enzymes with known mechanisms.

The paper identifies recurring 3D catalytic modules in enzymes using the M-CSA database, showing their conservation and role in catalysis and evolution.

This study examines conformational variation in enzyme catalytic residues using structural data to show that flexibility varies among enzymes and often involves non-bond-forming residues.