Protonate 3d tool

Manufactured by Chemical Computing Group

Sourced in Canada

Protonate 3D is a tool for adding hydrogen atoms to molecular structures in three-dimensional space. It is designed to facilitate the preparation of molecular models for computational chemistry and molecular modeling applications.

Automatically generated - may contain errors

Lab products found in correlation

Discovery studio 2, by Dassault Systèmes (1 mentions) Discovery studio 4, by Dassault Systèmes (1 mentions)

2 protocols using protonate 3d tool

Nrf2 Molecular Docking Simulations

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Molecular docking simulations were used to explore the potential interaction of FA-97 on Nrf2. The crystal structure of Nrf2 (PDB: 6QMC) was prepared by the Protonate 3D tool in MOE (version 2010.10, Chemical Computing Group Inc. Montreal, Quebec, Canada, 2010), and all the water molecules were removed. Hydrogen atoms were added using MOE. The structure of FA-97 was modeled and minimized in MOE. Docking simulations were carried out in the CDOCKER module implemented in Discovery Studio 2.5.5 (version 2.5, Accelrys Inc., San Diego, CA, 2009).

Wan T., Wang Z., Luo Y., Zhang Y., He W., Mei Y., Xue J., Li M., Pan H., Li W., Wang Q, & Huang Y. (2019). FA-97, a New Synthetic Caffeic Acid Phenethyl Ester Derivative, Protects against Oxidative Stress-Mediated Neuronal Cell Apoptosis and Scopolamine-Induced Cognitive Impairment by Activating Nrf2/HO-1 Signaling. Oxidative Medicine and Cellular Longevity, 2019, 8239642.

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Molecular Docking of Wogonoside on Gli1 and SMO

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Molecular docking simulations were used to explore the potential interaction of wogonoside on Gli1 or SMO. The crystal structure of Gli1 (pdb code: 5ED2) and SMO (pdb code: 4N4W) were prepared by the Protonate 3D tool in MOE (version 2010.10, Chemical Computing Group Inc. Montreal, Quebec, Canada, 2010) and all the water molecules were removed. Hydrogen atoms were added using MOE. The structure of wogonoside was modeled and minimized in MOE. Docking simulations were carried out in the CDOCKER module implemented in Discovery Studio 4.0 (version 2.5, Accelrys Inc., San Diego, CA, 2009).

Huang Y., Fang J., Lu W., Wang Z., Wang Q., Hou Y., Jiang X., Reizes O., Lathia J., Nussinov R., Eng C, & Cheng F. (2019). A Systems Pharmacology Approach Uncovers Wogonoside as an Angiogenesis Inhibitor of Triple-Negative Breast Cancer by Targeting Hedgehog Signaling. Cell chemical biology, 26(8), 1143-1158.e6.

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