This study allowed for the definition of a computational strategy to analyze the structure of the σ1 Receptor based on a combination of 3D pharmacophore-based docking and MM/PBSA free energy of binding scoring. modeFRONTIER demostrated to be a powerful tool to automate and optimize the coupling between docking and Molecular Dynamics codes, helping in providing evidence that these in silico models can be useful for virtual screening of new σ1 ligands.
In this study, multilevel modeling was used to demonstrate that complete dendron degradation would be necessary for effective DNA release. The choosen integrated experimental and theoretical approach has provided a unique insight into the way in which gene delivery vectors can approach cellular barriers to gene delivery. The entire MD simulation and data analysis procedure was optimized by integrating molecular modeling tools in modeFRONTIER.
Two peptides has been identified as valuable starting point for designing the first class of small molecules endowed with ELAV-like stabilizing effects, which could represent a highly innovative therapeutic tool. modeFRONTIER has been integrated with AMBER 11 to automate and optimize the complex workflows typically related to molecular dynamics simulations.
With modeFRONTIER, scientists and researchers are able to reduce experimental time, to streamline data assessment and to automate processes, by drawing on well-established engineering optimization and numerical modeling technologies.