Cheminformatics and Metabolism Team - Research

Over the past years my group founded and developed the Chemistry Development Kit (CDK), the now leading open source Java library for structural chemo- and bioinformatics [20,14]¹ Today, the toolkit is developed by us and more than 20 contributors in academia and industry world wide.
The CDK covers a wide range of functionality needed for performing virtual compound screening, property prediction and many other tasks of molecular informatics. In addition to its virtues for developing open systems in structural bioinformatics, its value for teaching cannot be overestimated. With 90.000 non commenting code statements (NCSS) in over 9000 methods in 900 classes, the CDK provides a basis for studying hands-on examples for the standard algorithms used in handling and modifying molecular structures as well as for calculating their properties, written in a modern object oriented language, using commonly accepted design pattern.

JChemPaint (or JCP for short here) is the editor and viewer for 2D chemical structures developed using CDK. [11]¹
It is implemented in several forms: a Java application and two varieties of Java applet. It can also be used as a component to embed in other applications. JCP has well tested an user-friendly interface. Its behaviour is consistent in the application and the applet. Some of the features offered are:

Drawing and deletion of single, double, triple and stereo bonds. Ring templates (3-8 atoms) with one-click attachment. An extensive template library. Colouring of atom types, and other rendering settings. Editing of atomic charges, isotopes and hydrogen count. Loading and saving of structures in Chemical Markup Language (CML) and as MDL MOL files and SDF files (loading only). Automated Structure Layout, also known as Structure Diagram Generation. Loading structures from the Internet using CAS or NSC number. Normalization of structures, currently limited to aromaticity detection. Saving bitmap pictures of the structures. Saving structures as graphics (PNG, BMP, Scalable Vector Graphics (SVG)). Postscript printing.

Figure 2: A structure shown in the Version 3.0 of the JCP applet.

More information, code examples, downloads, developer resources etc. can be found in the JChemPaint wiki.

The amount of novel basic research to be performed while developing the CDK goes significantly beyond what is to be expected from what looks like a pure infrastructure project. Questions of how to perceive aromaticity, perform fingerprinting of structures or define pharmacophore queries are often researched and published in CDK context for the first time.

OrChem is an Oracle database chemistry plug-in using the CDK [27]¹
For chemistry databases, various commercial "cartridges" exist that facilitate searching and analyzing chemical data. OrChem also provides functionality like this, but is not a cartridge. It doesn't need Oracle's extensibility architecture because its Java components run as Java stored procedures inside the Oracle standard JVM (Aurora).

More information can be found on the OrChem sourceforge home page.

Figure 1: Version 2.2 of Bioclipse (http://www.bioclipse.net) showing a 3D structure. A group is selected in the outline (right) and highlighted. The JavaScript console (bottom) offers interaction with the visualisation.

In collaboration with Jarl Wikbergs group at the University of Upsala, Sweden, we have founded the Bioclipse project (http://www.bioclipse.net) to build a plug-in based, rich client desktop workbench for Molecular Informatics [21]1 Bioclipse has won the JAX conference audience award for important European contribution to the development of Eclipse in the year 2006. On November 2007, we received the special price of the jury in the 4th edition of the Trophées du Libre. While Upsala currently expands Bioclipse's functionality towards Proteochemometrics capabilities, my group is working on plugins for spectrum handling, database editing and to extend Bioclipse's Systems Biology capabilities.The spectrum facilities are grouped in the Speclipse feature. The integration of an Systems Biology Markup Language (SBML) editor and the integration of metabolomics simulations will be the next step. Bioclipse will be the first state-of-the-art, user-friendly open desktop application for performing System Biology Simulations.

JCAMP-DX

The JCAMP-DX project is the reference implemention of the IUPAC JCAMP-DX spectroscopy data standard. It implements a parser and a writer to convert JCAMP-DX files to Java objects.