Chemical Properties Estimation Software System
Modules and Editions
ChemProp is not a single piece of software, but comprises several different modules. The availability of them, and thus of the features described here, may depend on a particular edition. Currently, there is a public free edition based on developments within the former EU Integrated Project OSIRIS. Furthermore, there is a professional version covering all features including batch processing in terms of QSAR runs for compound lists.
Structural input of one or many molecules is achieved either by means of a graphical molecule editor, via SMILES strings, input or compilation from MDL or SMD formatted molecule files, InChI codes and keys, some XML formats (CML, IUCLID), or by queries within the integrated structure database – e.g. name, registry number, property profile, substructures. There are modules to edit and visualise molecule compilation, for automated classification according to compound classes, and for structure related database searching.
Methods and calculations
Methods within ChemProp are implemented in a very flexible form, allowing for regular updating and extension according to the scientific progress.
In principle, the system contains a large number of calculation methods (from literature and UFZ developments) for environmentally relevant physical-chemical compound properties – partitioning properties, pure compound descriptors and properties, and even degradation rates at least in a simple manner –, environmental fate (e.g., BCF, BAF, fugacity models), ecotoxicity, and toxicity.
The implemented techniques are usually based on 2D structures including an automated substructure search. Prominent model types are fragment models, Abraham type LSER equations, read-across approaches based on atom-centred fragments, and models employing topological indexes as e-states.
Moreover, incorporated calculation models have access to the internal databases providing a number of experimental properties and descriptors.
There is a particular remark to the model applicability and reliability. As far as possible, the implemented models are accomplished by tools to characterise the applicability domain in terms of property and chemical space, and to provide uncertainty estimations.
Basically, it is possible to integrate any third-party software for particular cases, as long as this software is able to be run automatically, and provides a defined I/O interface for that reason. In any way, data and other calculation results may be imported from files and even from the clipboard if appropriate for the respective model implementation.
For the majority of property estimation models, particular pre-defined techniques and parameters can be applied, but also replaced by individual settings and adaptations. The calculations may be performed either as interactive tasks or as batch run, in the latter case series of property calculations for series of compounds will run fully automated without any user input after submission of the complete job to the ChemProp system. Profiles containing compilations of such tasks may be defined and stored for later usage.
There is a module for the access to external SQL compatible ODBC sources. In consequence, any data can hold in external databases from easy-to-use spreadsheet software to sophisticated database servers. ChemProp provides access to these data with respect to chemical structures, including substructure search tools and structure retrieval based on particular search results in external databases.
The primary result output of ChemProp are formatted tables in HTML visualised in an internal browser. Import to usual spreadsheet software is supported. In the default single-compound model, additionally a report in pdf format is created automatically.
Pure text output (ASCII), additional background information on calculation and model details as well as visualisation of substructure search results is available. Furthermore, basic statistical analyses including respective plots and compound class specific analyses (either user-specified or fully automated) are offered by the ChemProp system.
Documents and Help
Beside technical help on the ChemProp modules, there are documentations on the implemented calculation methods including information on alternatives and parameters as well as references including links to web resources.
For training purposes, an extensive tutorial is available. Training courses will also be held.