User-centric design of a 3D search interface for protein-ligand complexes

• Published in: Journal of computer-aided molecular design 2024-12, Vol.38 (1), p.23, Article 23
• Main Authors: Diedrich, Konrad, Ehrt, Christiane, Graef, Joel, Poppinga, Martin, Ritter, Norbert, Rarey, Matthias
• Format: Article
• Language: English
• Subjects: Animal Anatomy; Binding Sites; Chemistry; Chemistry and Materials Science; Computer Applications in Chemistry; Databases, Protein; Graphical user interface; Histology; Ligands; Models, Molecular; Morphology; Physical Chemistry; Protein Binding; Protein Conformation; Proteins; Proteins - chemistry; Proteins - metabolism; Queries; Search Engine; Search engines; Software; User-Computer Interface
• ISSN: 0920-654X; 1573-4951; 1573-4951
• DOI: 10.1007/s10822-024-00563-3

In this work, we present the frontend of GeoMine and showcase its application, focusing on the new features of its latest version. GeoMine is a search engine for ligand-bound and predicted empty binding sites in the Protein Data Bank. In addition to its basic text-based search functionalities, GeoMine offers a geometric query type for searching binding sites with a specific relative spatial arrangement of chemical features such as heavy atoms and intermolecular interactions. In contrast to a text search that requires simple and easy-to-formulate user input, a 3D input is more complex, and its specification can be challenging for users. GeoMine’s new version aims to address this issue from the graphical user interface perspective by introducing an additional visualization concept and a new query template type. In its latest version, GeoMine extends its query-building capabilities primarily through input formulation in 2D. The 2D editor is fully synchronized with GeoMine’s 3D editor and provides the same functionality. It enables template-free query generation and template-based query selection directly in 2D pose diagrams. In addition, the query generation with the 3D editor now supports predicted empty binding sites for AlphaFold structures as query templates. GeoMine is freely accessible on the Proteins Plus web server ( https://proteins.plus ).