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Our case studies

The genetic algorithm was trained with 3 protein systems and their respective congeneric ligand series. These are as follows:

p38alpha:

13 ligands derived from 4-(3-benzoylamino-6-methyl-anilino)pyrimidines

Thrombin (PDB):

77 ligands derivated from 3-amidinophenylalanine

Thrombin (GaMD):

86 ligands derivated from 3-amidinophenylalanine

The results show R2 correlations above 0.6 for all case studies, except for Thrombin with the 77 ligands. This is due to the low structural variability of the Thrombin binding site. To address this, new conformations were generated using Gaussian Accelerated Molecular Dynamics (GaMD).

Run our three case studies by going to the "Submit a Job" section and choosing one of the three options. The "VINA" and "Other docking software" buttons are designed to analyze results obtained from the VINA software or other docking software. In contrast, the "Excel" button enables you to analyze docking results without considering the three-dimensional structures of proteins and ligands, focusing solely on correlating experimental activities with computational energies. Finally, click on 'Download example' and upload the resulting file (ZIP or Excel) in the first field of the form. For more information, refer to the video in the bottom right corner.

Main differences when analyzing results obtained from VINA, Other docking software, and the Excel file.

Button Inputs Find the best correlation between activities Analysis for results of any docking software 3D visualization of protein-ligand complexes Results in tables and graphs Download results in CSV formats Download results in PDB, SDF/MOL formats
VINA ZIP (CSV, PDBQT and PDB)
Other docking software ZIP (CSV, SDF/MOL and PDB)
Excel

Excel

Link to the results of the correlation analysis for our case studies

Output visualization

Below are the results for the congeneric set of 86 ligands derived from 3-amidinophenylalanine in six thrombin conformations generated by GaMD. The correlation plot is on the left, while the 3D visualizer of the protein-ligand complex is on the right.

Reset zoom
Click on a point on the graph and see which protein residues the ligand comes into contact with. You can also zoom in and pan the graph data.
The colors represent a conformation of the protein. In contrast, each dot is the optimized binding pose for each ligand. Click on the legend to hide or show the ligands bound to that particular conformation.
Complex: Protein-Ligand
The orange-colored amino acids, represented as sticks, form hydrogen bonds with the ligand, which is colored grey. Hover over the amino acids to identify them. On the other hand, you can also rotate, zoom, and pan the 3D view.