Matthew M. Copeland

Open and Hybridized: The Topology of Chloroplast Barrel Proteins

The paper introduces COB, a database of chloroplast outer-envelope beta-barrel proteins, revealing structural and functional diversity across plant species.

Human Metalloenzymes Are Disproportionately Linked to Disease: The HEAM Structural Annotation Resource

The paper introduces HEAM, a dataset of human metalloproteins annotated for metal-binding sites and catalytic function, showing metalloenzymes are enriched in disease-related variants and pathways.

Simulation of cell-size systems at long timescales with flexible protein structures

The paper introduces a docking-based simulation method that combines rigid-body approximations with flexible protein structures to model macromolecular interactions in crowded cellular environments over long timescales.

Counting strands in outer membrane beta-barrels

The paper introduces an algorithm to accurately count strands in bacterial outer membrane beta-barrels, achieving 97% accuracy on 571,760 structures from AlphaFold2.

General Features of Transmembrane Beta Barrels from a Large Database

The paper creates a large, high-quality database of bacterial transmembrane beta barrels using co-evolution data and presents a new algorithm with high accuracy for identifying these proteins.

MAHOMES II: A webserver for predicting if a metal binding site is enzymatic

The paper improves a method to predict enzymatic metal binding sites using machine learning and computationally generated structures, achieving high precision and recall.