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

Geomfinder 2.0 is an enhanced version of our previous algorithm for the discovery of conserved 3D patterns among protein structures [1]. 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 (185x speedup at best compared to previous version), allowing the exploration of larger number of quaternary structures in a reasonable amount of time.

Server information:
  • 32 Intel(R) Xeon(R) CPU E5-2683 v4 @ 2.10GHz with Hyper-Threading (64 threads total).
  • 252 GB RAM.
If you have any question about Geomfinder, please send us an email to ganunez@utalca.cl

[1]
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).
https://jcheminf.biomedcentral.com/articles/10.1186/s13321-016-0131-9

Web site: http://geomfinder.appsbio.utalca.cl/