Michael Schroeder

This study evaluates how well three structural alphabets retain fold-level information compared to full-structure comparisons using TM-scores as a reference.

The paper benchmarks a new substitution matrix derived from AlphaFold-predicted structures against existing matrices, finding similar performance and highlighting the diminishing role of substitution matrices with more sequence data.

The paper uses PLIP to analyze structural data of drug-target interactions, revealing insights into the design principles of drugs targeting protein-protein interactions.

The paper uses AlphaFold to analyze the structure of Rad52 superfamily proteins across species, confirming their orthology and structural similarities.

The paper evaluates secondary structure's effectiveness in remote homology detection and finds a simple string comparison on secondary structure performs nearly as well as tertiary structure alignment.

The paper develops a multiscale computational model to understand the regulation of aquaporin 2 recycling and identifies cAMP compartmentalization as a key mechanism regulated by protein kinase A.

The paper identifies mutations in bdcA and valS associated with quinolone resistance in wastewater E. coli using genome-wide association analysis.

This study characterizes how aminoacyl-tRNA synthetases distinguish amino acids using computational analysis of crystallographic structures, revealing the role of binding site composition, non-covalent interactions, error correction, and steric effects.

This paper identifies ibrutinib as a VEGFR2 inhibitor through structure-based drug repositioning, revealing its polypharmacological action beyond BTK.

The paper evaluates drug repositioning approaches by analyzing 100 drugs, 200 targets, and 300 indications, finding that disease and target-centric methods dominate over drug-centric ones.

The paper introduces a Structural Relevance (SR) score to assess contact importance in protein structure prediction, improving resilience to false positives and reconstruction fidelity.

The paper identifies features of Early Folding Residues (EFR) in proteins using structural data, showing they differ from functional residues and provide insights into protein folding and design.

The paper characterizes the genomic diversity of multi-drug resistant Escherichia coli in wastewater, finding high genetic variation and resistance/virulence genes.

The paper identifies two distinct ATP binding motifs in aminoacyl tRNA synthetases (aaRS) and links their structural features to evolutionary hypotheses about the origin of these enzymes.