Molecular design procedures, such as drug design and protein engineering’ are complex processes, largely benefiting from computational resources but also from human analysis. In drug design, for example, a costly iterative loop involves simulations requiring long computation times, followed by a data analysis phase, which is conducted by domain scientists using numerical analysis and visualization tools. Once some clues favoring or hindering binding have been understood, the ligand is modified by taking into account these clues, and another iteration is performed. In typical cases, computer simulation times range from hours to weeks, depending on the complexity of the molecules and the methods used. Recent advances have led to a reduction in computation time by exploiting modern supercomputers [7] in combination with modern simulation algorithms [33]. These advances in parallel computation thus allow for the computation of many simulation paths at the same time. This increase in available data also implies that the requirements for analysis tools become more demanding.