Computational protocol: A molecular modeling based screening for potential inhibitors to alpha hemolysin from Staphylococcus aureus

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Protocol publication

[…] For virtual screening purpose, we used PyRX software []. PYRX includes AutoDock [] andAutoDockvina [] and its scoring function is based on Lamarckian genetic algorithm. More information about Lamarckian scoring function is provided in supplementary data. In this research we used AutoDockVina for molecular docking method. Before initiation of docking operation charge calculated and assigned to protein and ligand structures by AutoDockVina software. Also a big docking radius with a volume of 30 Å and coordinate of X: 31.25, Y: 24.75 and Z: 28.04 was used to cover interacting area of monomers. For simulation of biological condition, docking operation was performed in the presence of water molecules and neutralizing ions. [...] Successive hits of virtual screening data were then analyzed regarding liberation, absorption, distribution and metabolization properties. To do this, FAFDrugs3 web server was used []. The ligands were checked for ADME properties in optimal descriptors (hydrogen bonds, charge) in pH=7.4. Also the toxicity properties and probable accessorial targets of successive hits were analyzed by PROTOX web server []. […]

Pipeline specifications

Software tools PyRx, AutoDock, ProTox
Applications Drug design, Protein interaction analysis
Organisms Staphylococcus aureus
Diseases Lung Diseases, Staphylococcal Infections, Thrombocytopenia, Drug-Related Side Effects and Adverse Reactions