ChemSketch protocols

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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


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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 in pipelines

 (3)
2017
PMCID: 5404899
PMID: 28469408
DOI: 10.1177/1177392817701726

[…] been further modified based on our established research pipeline.– in this research, we used several kinds of offline and online software. molecular operating environment (moe) 2008.10,, acd/labs chemsketch 12.01, perkinelmer chembiodraw 13.0, vegazz 3.0.5, caesa (computer-assisted estimation of synthetic accessibility, v2.4; symbiosis inc, lanham, md, usa), toxtree 2.5.0, and osiris property […]

2017
PMCID: 5720600
PMID: 29238276
DOI: 10.5423/PPJ.RW.04.2017.0084

[…] and mure ligases and pectate lyase, respectively (; ). their structures were used to generate the various compounds modified with the combinations of halogen elements (br, cl, f and i) using acd chemsketch (version 11, advanced chemistry development, inc., toronto, on, canada, http://www.acdlabs.com/), resulting in 291 and 52 compounds that are similar in their structure to penicillin […]

2015
PMCID: 4651419
PMID: 26617459
DOI: 10.4137/DTI.S31566

[…] by using bioinformatics tools., several online and offline software were used in this research. offline software used in this research were molecular operating environment (moe) 2008.10, acd/labs’ chemsketch 12.01, research collaboratory for structural bioinformatics (rcsb) protein data bank (pdb) ligand explorer 4.1.0, vega zz 3.0.5, and toxtree 2.5.0. the materials used in this research […]


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ChemSketch in publications

 (169)
PMCID: 5884940
PMID: 29651297
DOI: 10.3389/fpls.2018.00408

[…] 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 […]

PMCID: 5842552
PMID: 29514608
DOI: 10.1186/s12885-018-4050-1

[…] 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 […]

PMCID: 5850101
PMID: 29443884
DOI: 10.3390/cells7020013

[…] 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 [] […]

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

[…] 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 […]

PMCID: 5770468
PMID: 29339801
DOI: 10.1038/s41598-018-19298-x

[…] reverse-transcriptase inhibitor, lamivudine (3tc), was obtained from the nih aids reagent program (#8146). recombinant human egf was from invitrogen (#phg0314). chemical structures were drawn in chemsketch (acd/labs)., experimental procedures were performed on pbmcs, obtained with written informed consent from volunteer blood donors, in accordance with relevant guidelines and regulations […]


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