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Protocols

ChemSketch specifications

Information


Unique identifier OMICS_04958
Name ChemSketch
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Percepta Predictors Team

Additional information


A registration is needed to access to tools; Demo: http://webstore.acdlabs.com/software-solutions/acd-chemsketch/

Publication for ChemSketch

ChemSketch citations

 (193)
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Ginger (Zingiber officinale) phytochemicals—gingerenone A and shogaol inhibit SaHPPK: molecular docking, molecular dynamics simulations and in vitro approaches

2018
PMCID: 5879566
PMID: 29609660
DOI: 10.1186/s12941-018-0266-9
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[…] therapeutic ability as reported earlier [–]. The 2D structures of the selected phytochemicals were represented in (Fig. ). The corresponding 2D structures of the eight phytochemicals were sketched on ChemSketch (http://www.acdlabs.com/resources/freeware/ChemSketch/) and were subsequently, imported onto D.S v4.5 to generate their 3D structures.Fig. 1 […]

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Niclosamide Blocks Rice Leaf Blight by Inhibiting Biofilm Formation of Xanthomonas oryzae

2018
Front Plant Sci
PMCID: 5884940
PMID: 29651297
DOI: 10.3389/fpls.2018.00408
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[…] io folding simulation. Next, the chemical structures of niclosamide, bismerthiazol and probenazole were generated from the SMILES notation (Simplified Molecular Input Line Entry Specification) in the Chemsketch Software. The active sites of each protein were predicted by COFACTOR (). To explore the protein-ligand interactions, the molecular docking of niclosamide was carried out in Argus Lab 4.0.1 […]

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Molecular modeling, dynamics simulations, and binding efficiency of berberine derivatives: A new group of RAF inhibitors for cancer treatment

2018
PLoS One
PMCID: 5863970
PMID: 29565994
DOI: 10.1371/journal.pone.0193941

[…] ]. These 485 compounds were chosen and their SDF files were downloaded and prepared for docking. In addition to BBR derivatives, vemurafenib and ATP-Mg were used as controls in the present study. ACD/ChemSketch 12.01 was used for in silico ligand generation, and pdb-formatted files were prepared for all compounds. To prepare and optimize the ligands for docking, polar hydrogen atoms were inserted, […]

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Exploration for novel inhibitors showing back to front approach against VEGFR 2 kinase domain (4AG8) employing molecular docking mechanism and molecular dynamics simulations

2018
BMC Cancer
PMCID: 5842552
PMID: 29514608
DOI: 10.1186/s12885-018-4050-1
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[…] 50 ≥ 5000 nmol/L, +), that was adapted based on the IC50values. The same criteria were followed for the test set compounds. Their corresponding two dimensional (2D) structures were sketched using the ChemSketch (http://www.acdlabs.com/ resources/ freeware/ chemsketch/ Advanced Chemistry Development (ACD) Inc., Toronto, Canada) and were translated to their three dimensional (3D) structures adapting […]

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Linear Regression QSAR Models for Polo Like Kinase 1 Inhibitors

2018
PMCID: 5850101
PMID: 29443884
DOI: 10.3390/cells7020013
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[…] es studied here are provided as canonical SMILES notation in section. All file format conversions were performed with Open Babel for Windows []. The molecular structures were visualized with ACDLabs ChemSketch freeware []. The conformation-independent molecular descriptors were computed as follows. We used the Pharmaceutical Data Exploration Laboratory (PaDEL) freeware version 2.20 [] because it […]

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Viwithan, a Standardized Withania somnifera Root Extract Induces Apoptosis in Murine Melanoma Cells

2018
PMCID: 5822503
PMID: 29491636
DOI: 10.4103/pm.pm_121_17

[…] was employed to get docking and binding scores, which is implemented by Lamarckian genetic algorithm method. The ligand molecules, withanolides were designed, and the structure was analyzed using ACD/Chemsketch. The PRODRG server was used to minimize the energy of drug compounds and three-dimensional coordinates were prepared. The protein structure files for B-cell lymphoma 2 (BCL-2), B-cell lymph […]


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