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vsFilt is a new web server for structural filtration and virtual screening of compound libraries. It takes into account the molecular mechanism of protein targets and detects various types of interactions of tested compounds in modeled complexes (hydrogen and halogen bonds, ionic interactions, hydrophobic contacts, pi-stacking, cation-pi interactions), allowing the selection of specifically bound drug-like ligands. The vsFilt algorithm significantly improves the performance of virtual screening and can become a particularly important postdocking tool to facilitate drug discovery efforts. - vsFilt is available at https://biokinet.belozersky.msu.ru/vsfilt (and also at https://biokinet3.belozersky.msu.ru/vsfilt) and compatible with major browsers (Chrome, Firefox, Opera); - does not require registration; - provides the confidentiality of user data; - processes molecular libraries of up to 150 000 compounds; - results can be downloaded for a local use or operated online using a built-in 3D analysis tool. Here, we will consider issues relating to the integration of docking, structural filtration and molecular dynamics methods, and provide examples of the use of vsFilt in high-throughput virtual screening (development of next-generation inhibitors against influenza A virus neuraminidase; search for anticancer agents among derivatives and mimics of natural compounds).