Protein Design

The modeling team works in the development of two software tools: FoldX and ModelX.

FoldX is an empirical force field developed for the rapid evaluation of the effect of mutations on the stability, folding and dynamics of proteins and nucleic acids. The core functionality of FoldX is the calculation of the free energy of a macromolecule based on its high-resolution 3D structure. The FoldX tool-suite allows the calculation of the stability of a protein, calculation of the positions of the protons and the prediction of water bridges, prediction of metal binding sites and the analysis of the free energy of complex formation.

ModelX is a tool-suite for biomolecular modeling. Its based on the usage of fragment libraries as building blocks developed to predict or reconstruct biomolecules and its interactions. The design of ModelX relies on interacting fragments pairs (of protein, DNA, RNA) standing for an interaction that accurately models structural complexes and predicts the biomolecular binding regions of resolved protein structures. The tool includes a fast statistical force field computed from the distances found in the training datasets (one forcefield for each type of interaction) to quickly evaluate and filter 3D docking models. Docked templates are compatible with FoldX protein design tool-suite to identify the crystallized molecule sequence as the most energetically favorable in the majority of the cases. ModelX can be used to predict interface changes upon protein mutagenesis and by predicting binding regions and binding sequences on proteins crystallized in non bounded configuration, opening perspectives for the engineering of protein-biomolecule interfaces.