GeneoNet

The identification of binding pockets in proteins is crucial for understanding protein function, drug discovery, annotating protein function, predicting protein-protein interactions, and facilitating structural studies. ​ GENEOnet provides a foundation for advancing the knowledge of biological systems and developing new therapeutic strategies.​

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How it works

The GENEOnet approach features a small number of parameters, a higher transparency (explainability) of the results, and the possibility of knowledge injection. Within our method, the pocket detection step is also composed by a voxellization and scoring phase of the​ empty volume (non-protein), where all the detected protein pockets are ranked according to the score value and filtered out based on a threshold.​

AAPK1_HUMAN

5'-AMP-activated protein kinase catalytic subunit alpha-1

Results

GENEOnet incorporates knowledge such as lipophilicity, hydrophilicity, electrostatic, distances and polar information, necessary to identify a binding site, so we define a GENEO (Bergomi et al.,2019) for each chemical-physical parameter, which can identify areas with the best values for these values. ​ The software compute information, such as pocket’s location, volume, and their druggability scores (goes from 0 to 1.0, where 1.0 is a high druggable site), unabling molecular modelling studies.​

Binding pockets identification on two different kinase proteins. The orthosteric and the allosteric sites are reported in green and blue respectively.

Aurora kinase A

Aurora kinase A

Q13131

5'-AMP-activated protein kinase catalytic subunit alpha-1

Please insert here the pdb Structure

 

References

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