The group develops or contributes developing a range of computational resources, listed below.
DynamXL provides a means to compare experimental cross-linking data against protein structural information. DynamXL accounts for the ﬂexible nature of both protein and cross-linker molecules by (1) predicting the accessible space of amino acid side chains, (2) aggregating measures from multiple protein conformation (3) measuring distances with a powerful shortest path algorithm, Theta*. DynamXL has been developed by Matteo while in Benesch group, University of Oxford.
EM∩IM relates electron density maps, typically obtained from transmission electron microscopy (EM), with ion-mobility mass spectrometry (IM-MS) data. It allows the user to estimate collision cross sections from density maps, and thereby enabling the mutual correlation and validation of IM-MS and TEM. Further, the software provides a means to define an appropriate EM threshold value (“contour”), leading to a density map visualisation more representative of actual data. EM∩IM can be controlled by a Graphical User interface or interactively via Python commands. EM∩IM has been developed by Matteo while in Benesch group, University of Oxford.
Assemble! is a tool aimed at generating atomistic polymeric mixtures ready for simulation in Gromacs. Assemble! is developed in Python, and can be controlled both via terminal and a graphical user interface.
POWer is an open source optimization framework with Particle Swarm Optimization (PSO) and CMA-ViE engines at its core. POWer enables creating specific optimization tasks, and has been since used to solve problems in the context of integrative modelling, force field parameterization and function minimization. POWer has been developed by Matteo while in the Dal Peraro group, EPFL (Switzerland), currently further developing and maintaining it.