The ED/MD suite comprises some of NBD’s core structure-based drug design technologies. It has been developed in one of the most highly reputed simulation groups in Europe (M. Orozco group, Institute of Research in Biomedicine, Barcelona). The three main technologies are ED/MD, MDWeb and MoDel.
ED/MD is a simulation technology that allows to quickly perturb a binding site of a receptor of known 3D structure with the goal of generating alternative conformations for ensemble docking and virtual screening purposes.
MDWeb is a bundle of workflows for molecular dynamics simulations that streamline the build-up and analysis of trajectories, allowing the implementation of MD simulations in the high throughput regime.
MoDel represents one of the most extensive molecular dynamics trajectory libraries of proteins available. The original library, composed of 1700 MD trajectories of monomeric protein structures is being extended to families of therapeutic, pharmacological and toxicological interest.
Scientific References and Patent
- The technology is currently protected by an international patent application (WO2013050481).
- Application of Drug-Perturbed Essential Dynamics/Molecular Dynamics (ED/MD) [...] JCTC (2012).
- MDWeb and MDMoby: an integrated web-based platform for molecular dynamics simulations.
- MoDel (Molecular Dynamics Extended Library): a database of atomistic molecular dynamics trajectories. Structure (2010)