EasyVS is a web-based bioinformatics tool that simplifies the selection of the molecular library and its virtual screening . Users can easily perform virtual screening of compound libraries with some clicks.
EasyVS allows easy customization of docking parameters and visualization of docking results. It’s working is explained as follows.
- At first, a user has to upload a target protein structure or enter a PDB ID for the same.
- In the next step, it predicts possible binding pockets using Ghecom that is a grid-based pocket finder . At this step, users can adjust docking parameters including exhaustiveness, the number of poses, grid box size, or provide coordinates separately.
- In the next step, it requires a molecular library of compounds. The supported libraries Drugbank, ChEMBL, ZINC purchasable, and so on. The molecules can be filtered based on various properties including molecular weight, hydrogen donor, and hydrogen acceptors.
- The library is processed and the molecules are docked with the target protein using Autodock Vina .
- During docking, it allows users to visualize results simultaneously.
- Pires, D. E., Veloso, W. N., Myung, Y., Rodrigues, C. H., Silk, M., Rezende, P. M., … & Ascher, D. B. (2020). EasyVS: a user friendly web based tool for molecule library selection and structure-based virtual screening. Bioinformatics.
- Kawabata, T. (2010). Detection of multiscale pockets on protein surfaces using mathematical morphology. Proteins: Structure, Function, and Bioinformatics, 78(5), 1195-1211.
- Trott, O., & Olson, A. J. (2010). AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of computational chemistry, 31(2), 455-461.