Molecular docking studies were performed using the CDOCKER program, which is a grid-based molecular docking method with a CHARMm force field in the BIOVIA Discovery Studio 2017 R2. To determine the binding mode of virtual hits to the hotspot binding site of PrPC, the NMR structure of PrPC was retrieved form the Protein Data Bank (PDB ID: 1AG2). From the docked structure of the PrPC-GN8 complex, GN8 was located in the hotspot binding site of PrPC with key residues (Asn159, Gln160, Lys194, and Glu196). This was used to define the binding site of PrPC. All of the ligand binding poses were generated, and the results were scored by the LigScore1 scoring function in BIOVIA Discovery Studio 2017 R2. LigScore136 (link) is one of the scoring functions that accurately predict the binding affinity between ligand and protein. The predicted structures of the protein-ligand complexes were visualised using the PyMOL program (https://www.pymol.org/ ).
Biovia discovery studio 2017 r2
Manufactured by Dassault Systèmes
Sourced in France
BIOVIA Discovery Studio 2017 R2 is a comprehensive software suite for molecular modeling, simulation, and analysis. It provides a wide range of tools and features for drug discovery, materials science, and other applications involving molecular systems. The software enables users to visualize, analyze, and manipulate molecular structures, perform computational chemistry calculations, and model various biological and chemical processes.
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Lab products found in correlation
3 protocols using biovia discovery studio 2017 r2
1
Molecular Docking of PrPC Ligands
2
Modeling and Visualizing E-Cadherin Ectodomain Structures
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SS- and X-dimer structures consisting of full-length ectodomains (EC1 to EC5) of E-cadherin were modeled using BIOVIA Discovery Studio 2017 R2 (Dassault Systèmes) by fitting the EC1–EC2 parts of the full-length ectodomains (PDB ID code: 3Q2V chain A) (25 (link)) to both sides of the SS- and X-dimers formed by EC1–EC2 (PDB ID codes: 2QVF and 3LNH) (10 (link)), respectively. Based on these full-length ectodomain structures, pseudo-AFM images of the SS- and X-dimers (Fig. 2B and D and SI Appendix, Fig. S7A and D ) were produced using the laboratory-made analysis software FalconViewer based on Igor Pro-8 (WaveMetrics) by setting the paraboloid-shaped tip of the AFM probe with a tip radius of 0.5 nm. The images were processed using a low-pass filter with a cutoff frequency of 2 nm. A modified model structure of the X-dimer (shown in SI Appendix, Fig. S7E ) was created to orient the EC3–EC5 region more flatly on the substrate, by rotating the dihedral angle φ of Lys212 (in the EC2–EC3 linker) to 180°. Models of the ectodomains and dimers (Fig. 6 ) were produced using Blender 2.93.5 (Blender Foundation). The pseudo-AFM images obtained in this study were deposited in the Mendeley Data Repository (53 ).
3
Computational Docking of S6 and S6h to Bovine Serum Albumin
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The structure of BSA was obtained from the protein data bank (ID: 4OR0) [18 (link)], and the residues in the DBS II were relaxed after manually inserting the S6 into the DBS (replacing it with the bound naproxen). Then, the molecular docking was conducted to model the binding modes of S6 and S6h in BSA using the LibDock module of the BIOVIA Discovery Studio 2017 R2 (Dassault Systèmes; Vélizy-Villacoublay, France). Two and three poses were obtained for S6 and S6h, respectively. Among them, the top-ranked pose for each is described in the results.
This computational molecular docking was conducted only with BSA, because BSA binds S6h with the DBS II site alone according to the inhibition study inSection 2.7 . Conversely, HSA appeared to be complex in binding with the CTZ indicators. For simplicity, we preferably chose the BSA–S6h pair in the docking simulation in this study.
This computational molecular docking was conducted only with BSA, because BSA binds S6h with the DBS II site alone according to the inhibition study in
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