Geomfinder 2.0: An enhance and parallel algorithm for deep exploration and discovery of similar and druggable 3D patterns.

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. Geomfinder 2.0 is an enhanced version of our previous algorithm. Important improvements have been incorporated:

  1. Allows to compare quaternary structures.
  2. Allows to compare a list of pairs of structures.
  3. Allows to know how druggable is the zone where similar 3D patterns were found.
  4. The execution time has been significantly reduced allowing the exploration of larger number of quaternary structures in a reasonable amount of time.

If you have any question about Geomfinder, please send us an email to Gabriel Núñez-Vivanco ( or Alejandro Valdés-Jiménez (

[*] Núñez-Vivanco, G., Valdés-Jiménez, A., Besoaín, F. et al. Geomfinder: a multi-feature identifier of similar three-dimensional protein patterns: a ligand-independent approach. J Cheminform 8, 19 (2016).
[*] A. Valdes-Jiménez, M. Reyes-Parada, G. Núñez-Vivanco and D. Jiménez-González, "Parallel algorithm for discovering and comparing three-dimensional proteins patterns," in IEEE/ACM Transactions on Computational Biology and Bioinformatics, (2024).