PROCOGNATE: a cognate ligand domain mapping for enzymes. - Matthew Bashton; Irene Nobeli; Janet M. Thornton (Nucleic Acids Res., 2008)

Small Molecule Subgraph Detector (SMSD) toolkit. - Syed Asad Rahman; Matthew Bashton; Gemma L. Holliday; Rainer Schrader; Janet M. Thornton (J. Cheminformatics, 2009)

SPEAR: Systematic ProtEin AnnotatoR. - Matthew Crown; Natália Teruel; Rafael Najmanovich; Matthew Bashton (Bioinform., 2022)