Teams

Medical bioinformatics group of the Medical Proteome Center at the Ruhr University Bochum

Automated pipeline for generating residue-level lipid contact annotations from PDB structures. The workflow queries RCSB PDB for structures containing lipid chemical components (117 recognized codes), downloads original PDB files, calculates all-atom heavy-atom contacts at 4.0 Angstrom cutoff, clusters sequences at 30% identity using MMseqs2, and partitions into train/validation/test splits. Produces a complete dataset of 4,704 proteins with 8,055,325 annotated residues.

Research areas: - Structure, evolution and maintenance of telomeres and their roles in chromosome stability, DNA repair and plant speciation - Epigenetic mechanisms in the regulation of gene expression, chromatin assembly, genome stability and telomere homeostasis - Transcription, replication and DNA repair in the context of nuclear and nucleolar architecture

This team is dedicated to the development of the Meta-NanoSim tool: https://github.com/bcgsc/nanosim