Web Services for Molecular Docking Simulations

Evaluation of bioactive compounds of plants used in Mexico, to predict potential SARS-CoV-2 inhibitors: Analysis between two molecular docking servers

“…DT (https://dockthor.lncc.br/v2/) (da Silveira et al, 2019;Santos et al, 2020) tiene proteínas virales de SARS-CoV-2 específicas para realizar acoplamiento molecular. Por lo tanto, solo se carga la molécula de interés y se selecciona la proteína a evaluar.…”

“…El servidor DT utiliza el programa DT como motor de acoplamiento. El servidor web utiliza las instalaciones informáticas de la plataforma brasileña de alto rendimiento (SINAPAD) y la supercomputadora SDumont (da Silveira et al, 2019;Guedes et al, 2021). DT ha sido evaluado con otros programas de acoplamiento molecular para la eficiencia de las funciones de puntuación (Rerank > MolDock > PLANTS > AutoDock Vina > DT) (González-Paz et al, 2020), concluyendo que DT es inferior en este aspecto a AutoDock Vina (el motor utilizado por CDS).…”

Applying the bioisosterism strategy to obtain lead compounds against SARS‐CoV‐2 cysteine proteases: An in‐silico approach

“…In this context, there is a wide range of software available on the market. Out of more than 50 existing package programs, AutoDock Vina or simply Vina, a semi‐flexible docking software of simple parameter configuration and easy to use, has been one of the most utilized tools in the last decade for in‐silico simulations of the intermolecular interaction between small flexible ligands and rigid biomacromolecules with flexible side chains 19–22 . Therefore, approaches involving computational systems on a chemical scope facilitate a subsequent experimental stage 23 .…”

“…Out of more than 50 existing package programs, AutoDock Vina or simply Vina, a semi-flexible docking software of simple parameter configuration and easy to use, has been one of the most utilized tools in the last decade for in-silico simulations of the intermolecular interaction between small flexible ligands and rigid biomacromolecules with flexible side chains. [19][20][21][22] Therefore, approaches involving computational systems on a chemical scope facilitate a subsequent experimental stage. 23 Based on the information given above, the current scientific research proposes the use of the bioisosterism strategy through the MB-Isoster software, associated with molecular docking studies, through AutoDock Vina, for the in-silico development of innovative molecules that promisingly inhibit cysteine proteases of SARS-CoV-2 or that function as multitargets for the treatment of COVID-19, thereby having the potential of being furtherly developed as a medication administered orally.…”