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Vina30

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AutoDock vina30 is a molecular docking software that can predict how small molecules, such as drug candidates, bind to a target protein of known 3D structure. It is designed to predict the binding mode and affinity of a small molecule to a target protein. The software uses a scoring function to evaluate the predicted binding modes and select the most favorable one.

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Lab products found in correlation

Tools 1, by AutoDock (2 mentions) Vina 1, by AutoDock (1 mentions)

3 protocols using vina30

1

Computational Docking of Substrate to RdhA_NP

Cited 1 time
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Computational docking of the substrate 3,5-dibromo-4-hydroxybenzoic acid to RdhANP was performed using AutoDock vina30 (link). A doubly-deprotonated substrate model was optimized using the UFF force field with Gaussian 0931 . AutoDock Tools 1.5.632 (link) was used to assign hydrogens and Gasteiger charges to RdhANP. The substrate carboxy moiety was made rotatable, and the four residues Phe291, Tyr426, Lys488 and Arg 552 were made flexible. A docking grid with dimensions of 24 × 36 × 18 Å was used to include the entire active site/substrate binding cavity. The final docking conformation was chosen based on the conformation with the shortest substrate heavy atom to cobalamin Co distance. This conformation was 1.4 kcal/mol higher in energy than the highest scoring result.
Payne K.A., Quezada C.P., Fisher K., Dunstan M.S., Collins F.A., Sjuts H., Levy C., Hay S., Rigby S.E, & Leys D. (2014). Reductive dehalogenase structure suggests a mechanism for B12-dependent dehalogenation. Nature, 517(7535), 513-516.
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2

Computational Docking of Compounds with AChE and MAO-B

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To simulate dockings of 3, 4, and 5 with AChE and MAO-B, we used AutoDock Vina30 (link), which has an automated docking facility. To define enzyme binding pockets, we used active sites defined by a complex of AChE with 4-carbamoyl-1-(3-{2-[(E)-(hydroxyimino)methyl]-1H-imidazol-1-yl}propyl)pyridin-1-ium (LND) (PDB ID: 6O5V) and a complex of MAO-B with (R)-rosiglitazone (RGZ) (PDB ID: 4A7A). To prepare 3, 4, and 5 for docking simulations, we performed the following steps: (1) created 2D structures of the three compounds, (2) converted these 2D structures into 3D structures, and (3) performed energy minimization using the ChemOffice program (http://www.cambridgesoft.com). Docking simulations of AChE or MAO-B with 3, 4, and 5 were performed using AutoDock Vina 1.1.231 (link). Based on the docking results, we checked for possible hydrogen bonding interactions with bonding relaxation constraints of 0.4 Å and 10.0° using Chimera 1.15 program32 (link).
Oh J.M., Jang H.J., Kang M.G., Song S., Kim D.Y., Kim J., Noh J.I., Park J.E., Park D., Yee S.T, & Kim H. (2021). Acetylcholinesterase and monoamine oxidase-B inhibitory activities by ellagic acid derivatives isolated from Castanopsis cuspidata var. sieboldii. Scientific Reports, 11, 13953.
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3

Computational Docking of Substrate to RdhA_NP

Cited 1 time
Check if the same lab product or an alternative is used in the 5 most similar protocols
Computational docking of the substrate 3,5-dibromo-4-hydroxybenzoic acid to RdhANP was performed using AutoDock vina30 (link). A doubly-deprotonated substrate model was optimized using the UFF force field with Gaussian 0931 . AutoDock Tools 1.5.632 (link) was used to assign hydrogens and Gasteiger charges to RdhANP. The substrate carboxy moiety was made rotatable, and the four residues Phe291, Tyr426, Lys488 and Arg 552 were made flexible. A docking grid with dimensions of 24 × 36 × 18 Å was used to include the entire active site/substrate binding cavity. The final docking conformation was chosen based on the conformation with the shortest substrate heavy atom to cobalamin Co distance. This conformation was 1.4 kcal/mol higher in energy than the highest scoring result.
Payne K.A., Quezada C.P., Fisher K., Dunstan M.S., Collins F.A., Sjuts H., Levy C., Hay S., Rigby S.E, & Leys D. (2014). Reductive dehalogenase structure suggests a mechanism for B12-dependent dehalogenation. Nature, 517(7535), 513-516.
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