User-centric design of a 3D search interface for protein-ligand complexes.
2D query editor
3D search engine
AlphaFold
GeoMine
Molecular interactions
PoseEdit
Protein Data Bank
Protein-ligand complexes
Journal
Journal of computer-aided molecular design
ISSN: 1573-4951
Titre abrégé: J Comput Aided Mol Des
Pays: Netherlands
ID NLM: 8710425
Informations de publication
Date de publication:
30 May 2024
30 May 2024
Historique:
received:
03
04
2024
accepted:
17
05
2024
medline:
30
5
2024
pubmed:
30
5
2024
entrez:
30
5
2024
Statut:
epublish
Résumé
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 ).
Identifiants
pubmed: 38814371
doi: 10.1007/s10822-024-00563-3
pii: 10.1007/s10822-024-00563-3
doi:
Substances chimiques
Ligands
0
Proteins
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
23Informations de copyright
© 2024. The Author(s).
Références
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