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AMBIT specifications

Information


Unique identifier OMICS_33368
Name AMBIT
Software type Application/Script
Interface Command line interface, Application programming interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java
Database management system MySQL
Computer skills Advanced
Stability Stable
Maintained Yes

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Versioning


No version available

Maintainer


  • person_outline Nina Jeliazkova

Additional information


http://ambit.sourceforge.net/usage.html

Information


Unique identifier OMICS_33368
Name AMBIT
Interface Web user interface
Restrictions to use None
Programming languages Java
Database management system MySQL
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Nina Jeliazkova

Additional information


http://ambit.sourceforge.net/usage.html

Publications for AMBIT

AMBIT citations

 (12)
library_books

A confidence predictor for logD using conformal regression and a support vector machine

2018
J Cheminform
PMCID: 5882484
PMID: 29616425
DOI: 10.1186/s13321-018-0271-1

[…] having the calculated property acd_logd (calculated logD) at pH=7.4, resulting in 1,679,912 compounds. Standardization of chemical structures was performed by ambitcli version 3.0.2, which is part of AMBIT cheminformatics platform and relies on the CDK library [–].Standardization was performed using default settings except for the option ‘splitfragments’ that was set to TRUE. In this way, salt and […]

library_books

In silico toxicology: comprehensive benchmarking of multi‐label classification methods applied to chemical toxicity data

2017
PMCID: 5947741
PMID: 29780432
DOI: 10.1002/wcms.1352

[…] The applicability domain of a prediction model is ‘the theoretical space in which a model can make reliable predictions.’ We used Ambit Discovery tool, to define the applicability domain using the Euclidean distance to the Mean method. To determine the applicability domain, we entered the training compounds along with their gen […]

library_books

The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching

2017
J Cheminform
PMCID: 5461230
DOI: 10.1186/s13321-017-0220-4

[…] DataBank [] databases. A number of such tools were initially developed using older versions of the CDK and are updated to new releases as they are made available. Examples include Bioclipse [, ] and AMBIT [–]. The CDK has also played a role in a number of chemical studies, such as finding the maximally bridging rings in chemical structures [], prediction of organic reactions [], and bioactivities […]

call_split

In silico toxicology: computational methods for the prediction of chemical toxicity

2016
PMCID: 4785608
PMID: 27066112
DOI: 10.1002/wcms.1240
call_split See protocol

[…] nicity, hepatoxicity, aquatic toxicity, reproductive toxicity, skin sensitization, and environmental toxicity. Examples of tools implementing read‐across are The OECD QSAR Toolbox, Toxmatch, ToxTree, AMBIT, AmbitDiscovery, AIM, DSSTox, or ChemIDplus. A detailed explanation of some of these tools is available in refs. , , , , , , , . […]

library_books

QSAR DataBank repository: open and linked qualitative and quantitative structure–activity relationship models

2015
J Cheminform
PMCID: 4479250
PMID: 26110025
DOI: 10.1186/s13321-015-0082-6

[…] choice of web-based integrated modelling environments is much broader. The list of model databases that also provide model development and/or prediction functionality includes OCHEM [], Chembench [], AMBIT2/OpenTox API [] and GUSAR from the NIH []. Additionally, notable collections of (Q)SARs are implemented and distributed as integral parts of stand-alone software solutions with free or limited a […]

library_books

Donor Control of Scavenging Food Webs at the Land Ocean Interface

2013
PLoS One
PMCID: 3694906
PMID: 23826379
DOI: 10.1371/journal.pone.0068221

[…] h-dune interface, forming a biological vector linking ocean productivity with terrestrial food webs. An important aspect of these predicted energetic linkages across habitat boundaries is the spatial ambit of trophic cross-boundary effects. Thus, future work may involve tracking raptor species to determine the spatial extent of marine subsidies at the land-ocean interface. […]

Citations

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AMBIT institution(s)
Ideaconsult Ltd., Sofia, Bulgaria

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