AMBIT

AMBIT is a database of chemical structures and cheminformatics, including machine learning and web services API. The AMBIT project includes several modules: AMBIT-SMARTS, Ambit-Tautomer, Ambit-GCM, Ambit-SLN, Ambit-SLN, and Ambit-SMIRKS.

Topic

Cheminformatics;Metabolomics;Protein structure analysis;Enzymes

Detail

  • Operation: Pathway or network analysis;Modeling and simulation;Query and retrieval

  • Software interface: Web user interface, command-line user interface

  • Language: Java

  • License: -

  • Cost: Free

  • Version name: Release: 3.1.0, development: 3.2.0

  • Credit: CEFIC-LRI EEM9.3-IC/EEM9.4, European Union’s Horizon 2020 Research and Innovation programme, Eawag (Switzerland) through a grant from the Swiss National Science Foundation.

  • Input: -

  • Output: -

  • Contact: -

  • Collection: AMBIT

  • Maturity: Mature

Publications

  • Linking LRI AMBIT chemoinformatic system with the IUCLID substance database to support read-across of substance endpoint data and category formation
  • Kaushik A, et al. miRMOD: a tool for identification and analysis of 5' and 3' miRNA modifications in Next Generation Sequencing small RNA data. miRMOD: a tool for identification and analysis of 5' and 3' miRNA modifications in Next Generation Sequencing small RNA data. 2015; 3:e1332. doi: 10.7717/peerj.1332
  • https://doi.org/10.1016/j.toxlet.2016.06.1469
  • PMID: -
  • PMC: -
  • Open Source Tools for Read-Across and Category Formation
  • Kaushik A, et al. miRMOD: a tool for identification and analysis of 5' and 3' miRNA modifications in Next Generation Sequencing small RNA data. miRMOD: a tool for identification and analysis of 5' and 3' miRNA modifications in Next Generation Sequencing small RNA data. 2015; 3:e1332. doi: 10.7717/peerj.1332
  • https://doi.org/10.1039/9781849732093-00408
  • PMID: -
  • PMC: -
  • How can structural similarity analysis help in category formation?
  • Jaworska J, Nikolova-Jeliazkova N. How can structural similarity analysis help in category formation? SAR QSAR Environ Res. 2007 May-Jun;18(3-4):195-207. doi: 10.1080/10629360701306050. PMID: 17514565.
  • https://doi.org/10.1080/10629360701306050
  • PMID: 17514565
  • PMC: -
  • The first eNanoMapper prototype: A substance database to support safe-by-design
  • Kaushik A, et al. miRMOD: a tool for identification and analysis of 5' and 3' miRNA modifications in Next Generation Sequencing small RNA data. miRMOD: a tool for identification and analysis of 5' and 3' miRNA modifications in Next Generation Sequencing small RNA data. 2015; 3:e1332. doi: 10.7717/peerj.1332
  • https://doi.org/10.1109/BIBM.2014.6999367
  • PMID: -
  • PMC: -
  • AMBIT RESTful web services: an implementation of the OpenTox application programming interface
  • Jeliazkova N, Jeliazkov V. AMBIT RESTful web services: an implementation of the OpenTox application programming interface. J Cheminform. 2011 May 16;3:18. doi: 10.1186/1758-2946-3-18. PMID: 21575202; PMCID: PMC3120779.
  • https://doi.org/10.1186/1758-2946-3-18
  • PMID: 21575202
  • PMC: PMC3120779
  • The eNanoMapper database for nanomaterial safety information
  • Jeliazkova N, Chomenidis C, Doganis P, Fadeel B, Grafström R, Hardy B, Hastings J, Hegi M, Jeliazkov V, Kochev N, Kohonen P, Munteanu CR, Sarimveis H, Smeets B, Sopasakis P, Tsiliki G, Vorgrimmler D, Willighagen E. The eNanoMapper database for nanomaterial safety information. Beilstein J Nanotechnol. 2015 Jul 27;6:1609-34. doi: 10.3762/bjnano.6.165. PMID: 26425413; PMCID: PMC4578352.
  • https://doi.org/10.3762/bjnano.6.165
  • PMID: 26425413
  • PMC: PMC4578352
  • The eNanoMapper database for nanomaterial safety information
  • Jeliazkova N, Chomenidis C, Doganis P, Fadeel B, Grafström R, Hardy B, Hastings J, Hegi M, Jeliazkov V, Kochev N, Kohonen P, Munteanu CR, Sarimveis H, Smeets B, Sopasakis P, Tsiliki G, Vorgrimmler D, Willighagen E. The eNanoMapper database for nanomaterial safety information. Beilstein J Nanotechnol. 2015 Jul 27;6:1609-34. doi: 10.3762/bjnano.6.165. PMID: 26425413; PMCID: PMC4578352.
  • https://doi.org/keep-10.3762/bjnano.6.165
  • PMID: 26425413
  • PMC: PMC4578352
  • Chemical Landscape Analysis with the Opentox Framework
  • Kaushik A, et al. miRMOD: a tool for identification and analysis of 5' and 3' miRNA modifications in Next Generation Sequencing small RNA data. miRMOD: a tool for identification and analysis of 5' and 3' miRNA modifications in Next Generation Sequencing small RNA data. 2015; 3:e1332. doi: 10.7717/peerj.1332
  • https://doi.org/keep-44264872
  • PMID: -
  • PMC: -

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