Geomfinder is an intuitive, flexible and ligand-independent web server for detailed estimation of similarities between all pairs of 3D patterns detected in any two given protein structures. We tested Geomfinder in almost 1.100 proteins, detecting 3D patterns and measuring their structural similarity in different subsets of these proteins. Thus:

  1. Geomfinder detected identical pairs of 3D patterns in a series of monoamine oxidase-B structures, which corresponded to the effectively similar ligand binding sites at these proteins;
  2. we identified structural similarities among pairs of protein structures which are targets of compounds such as acarbose, benzamidine, adenosine triphosphate and pyridoxal phosphate; these similar 3D patterns are not detected using sequence-based methods;
  3. the detailed evaluation of three specific cases showed the versatility of Geomfinder, which was able to discriminate between similar and different 3D patterns related to binding sites of common substrates in a range of diverse proteins.
If you found Geomfinder helpful, please cite: Gabriel Nuñez-Vivanco, Alejandro Valdés-Jiménez, F. B. M. R.-P. Geomfinder: a multi-feature identifier of similar three-dimensional protein patterns: a ligand-independent approach. Journal of Cheminformatics (2016).
Example Screencast
School of Bioinformatics Engineering | Department of Bioinformatics | Universidad de Talca | Talca, Chile