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Chemaxon's chemo-informatics toolkit integration into the Affectis Data Management System. Nkemdilim Uwaje and Markus Panhuysen 1 – Affectis Pharmaceuticals * Kraepelinstr. 2 * 80804 Munich / Germany -. Abstract. Data Management System Architecture.

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Chemaxon's chemo-informatics toolkit integration into the

Affectis Data Management System

Nkemdilim Uwaje and Markus Panhuysen1

– Affectis Pharmaceuticals * Kraepelinstr. 2 * 80804 Munich / Germany -


Data Management System Architecture

We developed a Java-/PSQL based data management solution for our R&D. Sources of our data are as diverse as immunohistochemistry and in situ hybridization experiments, in vitro screening and EC50/ IC50 curves (plate reader), in vivo experiments, and last but not least small molecule structures and whole compound libraries.

Here, we present the architecture of our growing data management system and delineate the integration of JChemBase and the Marvin API.

GUI client




open field


forced swim



screening data

validation data

EC50 / IC50 specificity


GUI client

PostgreSQL Database Server

SSL connectivity

compound structures & fingerprints * compound properties *

pharmacological annotations *

assay / experimental metadata

GUI client

Compound Database





GUI client










Thick Clients

Java+Jchem Applets

Aim of the data management software is to integrate data from our different R&D groups, provide comprehensive access to the accumulating data, allow rapid analysis of structure activity relationships from the point of view of different assays and offer a customizable report functionality. The compound management aspect of our database was implemented using Chemaxon's JChemBase tools. The JChemBase developers API functionalities were integrated for the handling and presentation of chemical structures as well as for compound-related calculations.

Compounds are introduced into the database via JChemBase either by importing or drawing. Additional data can also be entered (physical properties, R&S, pharmacological action, batch data…). Screening results and other experimental data are stored in a searchable, sortable meta-data style. Graphic files and images are annotated with content-related searchable data.

Automated Data Integration

- Example: IC50 Data generated with Flex-Station II -

SAR Tools



raw data

SAR / Compound

Export functionality

GUI client



temporary storage of raw

data in database

Compare 3D structure of

two or more molecules

Data Analysis


registration of

meta data

Sort search results

according to activity

About Us

Future Directions

Affectis Pharmaceuticals AG (located in Munich / Germany) is a young biopharmaceutical company dedicated to development of innovative drugs for the treatment of psychiatric disorders. Our expertise runs from target identification, in vitro / in vivo target validation and behavioral pharmacology to assay development, compound screening and lead optimization. Our main programs are in preclinical development or clinical phase II, respectively. Additionally, we perform service research collaborations with big pharma (Mitsubishi Pharma, Organon).

The presented database serves as a starting point for further developments. We are currently working on the improvement of the report generation capabilities, and of the overall-performance of the software. In the future, data from external databases will be integrated / linked (PubChem etc.). Searches will not be restricted to our own compound database but optionally include public database searches. The user management will be optimized in a way that users with specific functions will have specific perspectives and defined rights to read/edit/create data points within the database. We plan to implement a “3D-SAR-Viewer” which will be used to simultaneously visualize the structure activity relationship for a large set of compounds.

1 contact for correspondence: [email protected]