ChemDraw protocols

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ChemDraw specifications

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Unique identifier OMICS_04971
Name ChemDraw
Software type Package/Module
Interface Command line interface
Restrictions to use License purchase required
Operating system Mac OS, Windows
License Commercial
Computer skills Advanced
Stability Stable
Maintained Yes

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ChemDraw in pipelines

 (5)
2018
PMCID: 5774476
PMID: 29391779
DOI: 10.2147/DDDT.S149973

[…] buildqsar program. preparation of the receptor protein and docking validation method was performed by using yasara (http://www.yasara.org), and preparation of the ligand was performed by using the chemdraw ultra 12.0.2 and marvinsketch programs. the molecular docking process was performed by using the plants/protein–ligand ant system. meanwhile, the pymol program (www.pymol.org) was used […]

2017
PMCID: 5327470
PMID: 28240326
DOI: 10.1038/srep43398

[…] was typed with the charmm force field and a binding sphere with radius of 15.0 å was defined through the original ligand (dama-colchicine) as the binding site. the crolibulin and 5k were drawn with chemdraw and fully minimized using the charmm force field. finally, they were docked into the binding site using the cdocker protocol with the default settings. and figures were prepared using pymol […]

2016
PMCID: 4866741
PMID: 27226709
DOI: 10.2147/DDDT.S101929

[…] the predicted structure was further evaluated by the molprobity server. finally, ramachandran outliers and poor rotamers were corrected by the wincoot tool., numerous online servers and tools (chemdraw, mcule, vega zz, osiris property explorer, molinspiration, cresset, pymol, discovery studio, autodocktools, and ucsf chimera 1.6) were utilized to design novel compounds that might […]

2015
PMCID: 5378903
PMID: 26323712
DOI: 10.1038/srep13637

[…] final 3d homology models of dpo3a were built according to their 3d structure and discrete optimised protein energy (dope) score., the 2d structures of small-molecule ligands were created using the chemdraw panel. the 3d conformation of the ligands were generated and optimised with the discovery studio with the merck molecular force field. the optimised energy and minimised conformation of dope […]

2014
PMCID: 4081090
PMID: 24920828
DOI: 10.1093/nar/gku486

[…] most major vibrational mode of the system under investigation) generated by the server were used for analysis., the figures in this paper were prepared using pymol (http://pymol.sourceforge.net), chemdraw (cambridge biosoft), coreldraw (corel), prism5 (graphpad software inc.) or excel (microsoft), and compiled in adobe photoshop., the atomic coordinates and structure factors of milb (residues […]


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ChemDraw in publications

 (367)
PMCID: 5945596
PMID: 29748546
DOI: 10.1038/s41598-018-25869-9

[…] export averaged mass spectra in text format. mass spectra were also analyzed by mass++ 2.7.4 software. the ms figures were generated by mass++ 2.7.4. chemical structures were drawn using perkinelmer chemdraw prime 15.101.144., the targeted ms/ms spectra were acquired using the qtrap 4000 mass spectrometer in enhanced-product-ion mode. while fixing an energy spread of 10 ev, collision energy […]

PMCID: 5933462
PMID: 29482950
DOI: 10.1016/j.bmc.2018.02.026

[…] under aerobic (replicating; maba) (ref. ) or non-replicating (lora) (ref. ) conditions, determined at the institute for tuberculosis research, university of illinois at chicago. cclogp calculated by chemdraw ultra v12.0.2. (cambridgesoft)., footnotes for table 1:ayield in the final ab/cd coupling step for the 6-br compounds, or (#) for the cyanation step for the 6-cn compounds. bmic90 (µg/ml); […]

PMCID: 5938390
PMID: 29765362
DOI: 10.3389/fmicb.2018.00825

[…] then 150 μm acetoacetyl-coa (sigma) to initiate the reaction. the decrease in absorbance at 340 nm was recorded over 5 min to reflect the consumption of nadph., tachyplesin iii was processed with chemdraw 11.0 according to the structure of tachyplesin i (pdb code 2rtv) and docked to the active site of fabg from e. coli (pdb code 1q7b) or staphylococcus aureus (pdb code 3sj7) with autodock4 […]

PMCID: 5928221
PMID: 29712980
DOI: 10.1038/s41598-018-25154-9

[…] of the relative membrane permeabilities the calculated logp values, also known as log kow for the log of the partition coefficient between octanol and water, were calculated using the software chemdraw professional 15.1. dmts was the most hydrophilic compound tested (log p = −0.21) while dbts was the most hydrophobic (log p = 3.43). dbts was immiscible with water, methanol and ethanol […]

PMCID: 5916927
PMID: 29695799
DOI: 10.1038/s41598-018-24980-1

[…] binding pockets and respective cavity volumes of homology models of type iii pkss were identified using biovia discovery studio 4.5., predicted-ligand/product library was generated using chemdraw software and ligands/products were prepared in biovia discovery studio 4.5 along with protein preparation for protein-ligand/product docking studies. protein ligand/product docking was done […]


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