Applied Bioinformatics Group

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Bioinformatics software packages (co-)developed by our lab

We are (co-)developing several large open source bioinformatics software packages for molecular modeling, systems biology, and computational proteomics. Please check out the latest versions of these.


OpenMS is a C++ framework for Proteomics currently under development in the groups of Prof. Reinert (FU Berlin) and Prof. Kohlbacher. For details contact Oliver Kohlbacher.


Fred 2 is an immunoinformatics framework for epitope detection and the successor of the original python package FRED.


BN++ (formerly known as 'BioMiner') is a software system in C++ for analyzing and visualizing complex biochemical networks and processes. BN++ was designed to simplify the implementation of tools for answering a broad range of interesting biochemical questions. BN++ is based on a new comprehensive, extensible and reusable data model capable of representing complex and diverse biochemical data in a unified fashion.


BALLView is a fully featured stand-alone application for molecular visualization and molecular modeling. Whether you just want to look at protein structures or want to minimize structures with AMBER or CHARMM force fields, this is the way to do it. Available under the GNU Public License (GPL) for most platforms, inlcuding Linux, Windows, and MacOS.


Rapid Software Prototyping can significantly reduce development times in the field of Computational Molecular Biology and Molecular Modeling. BALL (Biochemical Algorithms Library) is an application framework in C++ that has been specifically designed for this purpose. It provides an extensive set of data structures as well as classes for Molecular Mechanics, advanced solvation methods, comparison and analysis of protein structures, file import/export, and visualization.


CoMPAS - Comprehensive Meta Prediction and Annotation Services for Proteins: An all-in-one prediction tool that can be easily extended to include any SOAP/WSDL-enabled prediction servers. A concise user interface lets you use the results instantly for further analysis or publication.


CADDSuite - A flexible and open framework and workflow system for computer-aided drug design.