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Chemdraw professional 16

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ChemDraw Professional 16.0 is a software application used for the creation and visualization of chemical structures, reactions, and diagrams. It provides tools for drawing and editing chemical structures, as well as for generating various representations such as 2D and 3D models, and publication-quality images.

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Lab products found in correlation

9 protocols using chemdraw professional 16

1

Molecular Modeling of Huperzine A Analogs

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Structures
of HupA and its analogs were constructed in ChemDraw Professional
16.0 followed by three-dimensional (3D) structure transformation using
Chem3D Professional 10.0. All analogs were then energetically minimized
by Chem3D Professional 10.0 by using the MM2 force field to avoid
any steric clashes of the freely rotatable bond.
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2

Computational Screening of Doxorubicin Derivatives

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The ChemDraw Professional 16.0 was used to sketch the target compounds. Then, the target compounds, doxorubicin, and EVP were inserted into a single database and exposed to force field energy minimisation42 (link),43 (link).
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3

Silk Fibroin Extraction and Characterization

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Sodium alginate solution (0.5% and 1% w/v), gelatin type A solution (1–6% w/v), and silk fibroin solution (1–3% w/v) were prepared in Milli-Q water. Silk fibroin was extracted from the cocoons of the silkworm Bombyx mori.41 (link) ChemDraw Professional 16.0 was used to draw the chemical structures of the polymers, presented in ESI Fig. S1. For silk fibroin, briefly, cocoons were cut into small pieces. 5 g of cocoon pieces was boiled in 0.02 M sodium carbonate solution for 30 min. Following this the fibres were filtered out and washed thrice in distilled water and air-dried overnight. Dried fibres were dissolved in 9.3 M lithium bromide solution in a 1 : 4 volumetric ratio, over a period of 3–4 h with stirring, at room temperature. The dissolved silk fibroin (10 mL) was then dialyzed against 1 L Milli-Q water (with 6 changes) over a 48 h period using 10 K MWCO dialysis tubing (manufacturer). To determine the concentration of silk in solution, a small weighing boat was measured, and 0.5 mL of the silk solution was placed in the boat and allowed to dry at 60 °C. Once dry, the weight of the silk was determined and divided by 0.5 mL and the yielded weight per volume (w/v) percentage was calculated. Following this method, we obtained a yield of 3 ± 0.2%.
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4

Cheminformatics Analysis of Drug Molecules

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ChemDraw Professional 16.0 was used to create the two-dimensional chemical structures, saved for subsequent use. A structure-based search and a streamlined molecular input line entry mechanism are both supported by the drug-likeness and pharmacokinetics databases (SMILES). By using the SwissADME database, the SMILES notation of each drug was initially obtained. Each molecule’s SMILES notation was used to predict various cheminformatics-related features, establish molecular fingerprints, and assign IUPAC names. International chemical identifier (InChI) software version 1.06 obtained from IUPAC was used to generate InChI and InChI keys (Goodman et al., 2021 (link)).
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5

Molecular Docking of Curcumin and CB2R Agonist

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The protein data bank (RCSB) was used to obtain a G protein coupled CB2R (6KPC) crystal structure. The ChemDraw Professional 16.0 software was used to design a 2D structure of the ligands, i.e., curcumin and a selective CB2R agonist JWH-133. The molecular mechanics optimization of the 2D structures of the ligands into the 3D structures was performed using the Chem 3D 16.0 application of the same software. Further, for molecular docking, the Argus Lab 4.0.1 software was used. The grid with dimension X = 37.5236, Y = 22.4981, and Z = 20.6868 Å were assigned to cover the entire 3-dimensional active site of CB2R. Dynamic molecular docking was carried out on the active site of protein (CB2R). The binding energy was retrieved, and the CB2R–curcumin interaction was visualized using Discovery Studio 2016 software [21 (link),22 (link)].
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6

Ellagic Acid Structure Optimization

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The two dimensional structure of the selected ligand Ellagic acid was retrieved from ChemDraw Professional 16.0 software (Fig. 1), and it was saved in mol format. The optimised 3D Ellagic acid structure was generated through the energy minimisation process using Chem3D 16.0 software, and it was saved in pdb format (Figs. 2 and3).
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7

Molecular Docking Analysis of ABL Kinase-Imatinib Complex

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Crystal structure of the ABL kinase in complex with imatinib was obtained from Protein Data Bank (PDB: 1IEP); PT5 was built by ChemDraw Professional 16. Before the docking simulations, PT5 and 1IEP preparation included the addition of hydrogens, the assignment of bond order, and assessment of the correct protonation as previously described [46 (link),47 (link)]. The MOE 2019.01 software (Chemical Computing Group, Montreal, Canada) was employed for the preparation, interactive docking, visualization and the analysis procedures using its default parameters [48 (link),49 (link),50 (link)].
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8

Molecular Networking for Metabolite Annotation

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Molecular networking was generated using Global Natural Products Social Molecular Networking (GNPS; https://gnps.ucsd.edu; accessed on 23 May 2022) [33 (link)]. The preprocessed data were submitted to a feature-based molecular networking workflow (version 28.2) in GNPS [34 (link)]. The precursor-ion mass tolerance and MS/MS fragment ion tolerance were set to 0.02 Da. Edges in the network were created when a cosine score was above 0.7 with at least 6 matched fragment ions. The molecular network data were visualized by Cytoscape (version 3.8.0.). Annotated metabolites were collected, and structures were confirmed with their ion fragmentation from LC-MS/MS using ChemDraw Professional 16.
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9

Structural Analysis of T6PP Enzyme

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Root mean square deviation (RMSD) values of the α-carbons were calculated using the PDB Calculate Structure Alignment tool (23 ). The size of the active-site cavity was measured with Voidoo (24 (link)), and tunnels to/from the active site were determined using Caver (25 (link)). Molecular graphics were performed using UCSF Chimera (26 (link)) unless otherwise noted. UCSF Chimera was also used to determine hydrogen bonds (Find Hbond (27 )) or van der Waals interactions (Find Contacts (28 )) made between enzyme residues and ligand. Two-dimensional depictions were drawn in ChemDraw® Professional 16. Multiple sequence alignments were generated using Clustal Omega (29 (link)) and visualized with ESPript 3 (30 (link)). For conservational analysis, 80 sequences of T6PP from bacteria, fungi, plants, insects and nematodes were included (see supplement for list of UniProt IDs). Each sequence is manually curated by UniProt based on sequence analysis and experimental evidence from literature (31 (link)). Sequence identities were extracted from a multiple sequence alignment of Bm, Ce, Cn, Af, Ca, Ta, St, Mt, and Mm T6PP sequences.
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