Toxtree protocols

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Toxtree specifications

Information


Unique identifier OMICS_05024
Name Toxtree
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Unique identifier OMICS_05024
Name Toxtree
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for Toxtree

Toxtree in pipelines

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

[…] (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 explorer were the offline and online software that were used to conduct this research, respectively., in this study, the modified sah ligands and the standards […]

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

[…] 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 are sequence data and 3d structure of envelope protein of denv. these data are available online on national center of biotechnology information […]

2013
PMCID: 3668210
PMID: 23547944
DOI: 10.1186/1742-4682-10-22

[…] including hydrogen bonds and bond lengths were analyzed using swiss-pdbviewer v4.0 [], pymol software [], ucsf chimera [] and accelrys ds visualizer software []. the commercially available software toxtree (developed by idea consult ltd., sofia, bulgaria) was used for computer-based estimation of chemical toxicity []., multiple sequence alignment of veb-1 with per-1, ctx-m-16 and toho-1 […]


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Toxtree in publications

 (28)
PMCID: 5826228
PMID: 29515993
DOI: 10.3389/fchem.2018.00030

[…] and dermal pharmaceuticals and final products used in manufacturing, agriculture, and warfare (wilhelmus, ; kolle et al., )., verheyen et al. evaluated the existing qstr models in derek nexus, toxtree and case ultra for the prediction of skin and eye irritation/corrosion, and found that the performance of those models is unsatisfactory because of narrow applicability domain and low […]

PMCID: 5837273
PMID: 28525648
DOI: 10.1093/toxsci/kfx097

[…] freely available on several platforms such as the organisation for economic co-operation and development (oecd) quantitative structure-activity relationship toolbox () and the joint research center toxtree application (), it is only useful for acute toxicity endpoints and has a limited ability to assign a chemical class, meaning that many chemicals cannot be classified. further, the biological […]

PMCID: 5404899
PMID: 28469408
DOI: 10.1177/1177392817701726

[…] (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 explorer were the offline and online software that were used to conduct this research, respectively., in this study, the modified sah ligands and the standards […]

PMCID: 5848496
PMID: 29101769
DOI: 10.14573/altex.1710141

[…] value and the fitness of the parent dataset., repeat steps (3) and (4) for each feature in the dataset and choose the “fittest” features, repeat steps (2) through (5) until some terminal state., toxtree is one example of a classification tree used in a public computational model. it uses “reactivity alerts” as features that identify chemicals that have the potential to be reactants […]

PMCID: 5034616
PMID: 28316646
DOI: 10.1186/s13321-016-0164-0

[…] parameter that allows for a selection in the desirable trade-off between model sensitivity and specificity. the predictive performance of the ensemble model is compared with four in silico tools (toxtree, lazar, oecd toolbox, and danish qsar) to predict carcinogenicity for a dataset of air toxins (332 chemicals) and a subset of the gold carcinogenic potency database (480 chemicals). […]


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Toxtree institution(s)
European Commission, DG Joint Research Centre, Institute for Health and Consumer Protection, Ispra, Italy

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