Active Development and Maintanance

BEclear – Batch Effect Detection and Adjustment in DNA Methylation Data. – PLoS One (2016)

CompleXChange – Differential analysis of combinatorial protein complexes. – BMC Bioinformatics (2019)

DACO – A novel transcription factor complex prediction algorithm. – Bioinformatics (2014)

MCDS (Heuristic solution) – MCDS is a Cytoscape app that allows users to find an approximate MCDS solution in a directed graph. – BMC Systems Biology (2016)

MDS and MCDS (Optimal solutions) – Implementation of the ILP formulations for MDS and MCDS problems in the Sage software system using the glpk solver underlying gene regulatory networks. – BMC Systems Biology (2016)

MutaNET – MutaNET provides a NGS mutation calling pipeline and an automated analysis tool for coding regions, protein domains, regulation and transcription factor binding site information to analyse the potential impact of mutations on genes of interest. – Bioinformatics (2018)

PPICompare – PPICompare detects rewiring events in protein interaction networks.  – BMC Systems Biology (2017)

PPIXpress – PPIXpress constructs spicing-specific protein interaction networks from transcript expression data. – Bioinformatics (2015)

ProPores 2 – ProPores2 is a C++ command line tool for analysing pores (and cavities) in proteins. It is also available as a webservice. – Journal of Chemical Information and Modeling (2021)

Inactive Development

Brownmove – A many-particle Brownian-Dynamics simulation package.

EPOSBP – Ensemble of Pockets on Protein Surfaces with BALLPass. – Journal of Medicinal Chemistry (2007)

QVADIS – Java3D program package to characterize proton transfer pathways in biomolecules accounting for side chain flexibility and transfer kinetics.

Mebitoo – Mebitoo is a bioinformatics tool to embrace computational analysis methods with a uniform graphical user interface. Moreover, the software enables persistent storage with an incorporated database engine, which supports XML files for customized data structures. – BICoB (2015)

MolTPC – MolTPC provides a solution for fully automatic tautomer enumeration. – Journal of Computational Chemistry (2013)

PROPORES (PROtein PORE identification toolS) – PROPORES is a toolkit for identifying pockets, cavities and channels in protein structures, pore axis determination and opening potential gates between neighbouring pores. – Proteins: Structure, Function, and Bioinformatics (2012)

Q-HOP MD – The Q-HOP method is a semi-quantitative approach to study proton transport in biomolecular systems. It can efficiently explore proton transfer paths e.g., in proteins that consisting of many subsequent transfer events. – Journal of Chemical Physics (2001)

SnvDMiR – Associating the genomic  proximity of genetic variants with deregulated miRNAs and differentially methylated regions.  (R code)


Vesimulus – A molecular stochastic simulations of metabolic or signaling systems. – PLoS One (2010)