We are (co-)developing several large open source bioinformatics software packages for molecular modeling, systems biology, and computational proteomics.
QVADIS Java3D program package
Further information about the research part...
Brownmove, a many-particle Brownian-Dynamics simulation package
Vesimulus, molecular stochastic simulations of metabolic or signaling systems
TopoView (download here)
CESIP (cellular simulation package) in C++
SnvDMiR (Associating the genomic proximity of genetic variants with deregulated miRNAs and differentially methylated regions) ... download the source code in R