November 2020

The user can provide a set of conformations for the ligand or the protein or both. This allows, for example, to use a set of snapshots from a MD trajectory to define the conformational space that GPathFinder will explore.

March 2020

Bug fix: problems with the format of some .mol2 files, that produced an error like "ValueError: invalid literal for int() with base 10:" when saving the results of GPathFinder. Thanks to Manish K. from the Nagoya University for reporting it.

October 2019

New PCA analysis functionality. If you have a trajectory file (.dcd) of a molecular dynamics, you can now include low energy motions calculated throughout PCA analysis. GPathFinder would include those movements in its calculations.

September 2019

New smina scoring. Possibility of using its built-in scoring functions or making a custom file with your own one. Also allows to introduce your custom atom parameters file.

July 2019

• New summary.csv file in the output with score data of all the solutions.
• New format for the .pdb files of the output that can be imported as a MD movie in UCSF Chimera.
• New trajectory.pdb file in the output. For each solution, shows the trajectory of the ligand, taking its center as a reference.
• Command to lauch the program is now gpath run instead of gaudi run to ensure compatibility with GaudiMM.
• Similarity between solutions is calculated now at each generation, to avoid some cases where repeated or very similar solutions appeared, especially when using only clashes evaluation.