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AMBIT

Contact: Nina Jeliazkova

Categories: Descriptor calculation, Data access, Report generation

Exposed methods:

Description:

AMBIT is a software package for chemoinformatic data management, implemented by IDEA. The descriptor
calculation relies on CDK library, but also implement several descriptors , listed below, which are not available
from the library. The descriptor calculation is a separate module and packaged in ambit2-descriptors.jar,
which depends only on cdk library, core ambit module (ambit2-core.jar ) and ambit SMARTS (ambit2-
smarts.jar) implementation.

Consists of

  • a relational database database schema, allowing to store and query all relevant structure and property information, including data for toxicity endpoints from various sources and formats. Can handle very large number of structures efficiently
  • functional modules allowing a variety of evaluations flexible structure, similarity and other information retrieval. Used in both standalone and web (servlets/taglibs based) applications

Applications:

  1. Ambit Database tools 1.30 (Java, LGPL) (Standalone database query and management interface )
  2. Ambit Discovery (Java, LGPL) (Applicability domain assessment)
  3. Ambit Online (Demo application allowing to query AMBIT database online)
  4. QMRF Repository (Web based portal for submitting documents in QMRF format)
  5. AMBIT XT (Workflow based application )

AMBIT XT (Java, LGPL)

Objective: Develop an open source user friendly software, providing a set of functionalities to facilitate registration of the chemicals for REACH.

Under development, first release December 2008, final release July 2009

  • Built upon AMBIT
  • Workflow support (embedded workflow engine)
  • Modular application (flexible plug-in support)
  • Implements a set of workflows, defined by the industry (e.g. analogue identification, PBT assessment, etc.)

Database

  • Improved database schema

Data provenance

  • History of the origin and updates of the chemicals information.
  • Data quality
  • Easy way for comparison between different sources
  • Flexible storage for measured toxicological data for different endpoints
  • Easy way to extract all relevant information for a chemical; many formats available for toxicological data
  • Easy entry of complex structural alerts to facilitate grouping

Molecular descriptors

User interface and reporting

  • Recording of user actions
  • Improved data entrance and visualization
  • Reporting compatible with IUCLID 5

Type of Descriptor:

Various
ambit2.descriptors.PKASmartsDescriptor Acid dissociation constant, [LEE08]
ambit2.descriptors.SpherosityDescriptor Spherosity descriptor [TOD00]
7.1ambit2.descriptors.CrossSectionalDiameterDescriptor Crossectional diameter of a
molecule . Requires 3D coordinates
ambit2.mopac.DescriptorMopacShell A shell to calculate quantum chemical descriptors
by MOPAC ambit2.descriptors.FunctionalGroupDescriptor The presence of arbitrary
functional groups, defined as SMARTS pattern. Full support for SMARTS language,
including recursive SMARTS.
toxtree.descriptors. SubstituentsDescriptor Partial molar refractivity and Sterimol
descriptors of substituents, as found in [HAN95]
Similarity/distance calculations:
ambit2.similarity module encapsulates similarity calculations – all distance classes
implement the same interface. Supports pairwise similarity/distance,
similarity/distance to a set of points and similarity/distance based on nearest
neighbors
Tanimoto Distance, Atom Environments Distance, BinaryKernelDistance, Hamming
Distance, Levenstein Distance, MCSSDistance, Hellinger distance, Kullback – Leibler
distance between probability distributions

Interfaces: Standalone application, Website

Priority: Low

Development status: Production

Homepage: http://ambit.sourceforge.net

Dependencies:

Technical details

Data: Yes

Software: Yes

Programming language(s): Java, JSP

Operating system(s): Any

Input format: Multiple text formats, MySQL database, User interface

Output format: Multiple text formats, MySQL database, User interface

License: LGPL

References

References:
[HAN95] C. Hansch, A. Leo and D. Hoeckman, (1995) Exploring QSAR, hydrophobic, electronic and steric constants, ACS, Washington DC
[LEE08] Adam C. Lee, Jing-yu Yu, Gordon M. Crippen, (2008) pKa Prediction of Monoprotic Small Molecules the SMARTS Way, Journal of Chemical Information and Modeling, 48 (10), 2042- 2053
[TOD00] Roberto Todeschini, Viviana Consonni, Raimund Mannhold, Hugo Kubinyi, Hendrik Timmerman, Handbook of Molecular descriptors, 2000

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