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- Title
User-centric design of a 3D search interface for protein-ligand complexes.
- Authors
Diedrich, Konrad; Ehrt, Christiane; Graef, Joel; Poppinga, Martin; Ritter, Norbert; Rarey, Matthias
- Abstract
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 ProteinsPlus web server (https://proteins.plus).
- Subjects
GRAPHICAL user interfaces; BANKING industry; BINDING sites; SPATIAL arrangement; SEARCH engines; DNA-binding proteins
- Publication
Journal of Computer-Aided Molecular Design, 2024, Vol 38, Issue 1, p1
- ISSN
0920-654X
- Publication type
Article
- DOI
10.1007/s10822-024-00563-3