Software development

Most of our research is methodological and therefore requires the development of appropriate software. We have made all our research software publicly available, both to allow verification of our work and to provide useful tools to the scientific community. Our most widely used tools are the Molecular Modelling Toolkit (MMTK), a Python library for molecular simulation, and nMOLDYN, an analysis tool for Molecular Dynamics (MD) trajectories and the calculation of MD-based neutron scattering spectra.

Other software developed by the group includes:

• ScrewFrame/ScrewFit, a geometrical model for protein secondary-structure analysis
• ActivePapers, an infrastructure for packaging and publishing data, code, and documentation
• ScientificPython, a Python library for common tasks in scientific computing
• DomainFinder, an interactive program to analyze collective motions in large proteins
• DensityFit, tool for deforming protein structures to fit into a low-resolution density map from electron microscopy
• HYDROLIB, a Fortran library for the accurate evaluation of hydrodynamic interactions in colloidal suspensions