Active Development and Maintanance
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)
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)
Brownmove – A many-particle Brownian-Dynamics simulation package.
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)
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)