Ioannis G. Riziotis

Determinants of cysteine coverage by chemoproteomics

This study identifies factors governing cysteine detection in chemoproteomics using machine learning and statistical filtering, showing that peptide properties and abundance are key determinants.

Investigating Enzyme Function by Geometric Matching of Catalytic Motifs

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.

A global survey of intramolecular isopeptide bonds

The paper identifies and characterizes intramolecular isopeptide bonds in protein domains across organisms, revealing their structural and functional significance.

Robust proteome profiling of cysteine-reactive fragments using label-free chemoproteomics

This paper develops a label-free chemoproteomics platform to profile cysteine-reactive fragments, identifying over 400 ligand-protein interactions in two cell lines.

Isopeptor: a tool for detecting intramolecular isopeptide bonds in protein structures

Isopeptor detects intramolecular isopeptide bonds in protein structures using structure-guided template matching and logistic regression, achieving high recall and precision on a curated PDB subset.

Paradigms of convergent evolution in 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: An Automated Tool to Propose Catalytic Mechanisms of Enzyme Reactions

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

The 3D modules of enzyme catalysis: deconstructing active sites into distinct functional entities

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

Conformational variation in enzyme catalysis: A structural study on catalytic residues

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.