A new high speed and accurate approach of structure based drug design is offered to molecular modelers, crystallographers and medicinal chemists
Macromolecules surface similarity detection with MED-SuMo at PDB scale is a technology breakthrough to discover a wealth of drug design data. MED-SuMo is a state of the art technology to search into 3D databases, find similar binding surfaces and generate 3D superpositions based on common surface chemical features and similar shape.
Superposing macromolecules is a basic and powerfull tool for new drug design applications and for improving standard techniques:
Functionnal-annotation - Site detection
Collect bioisosteric data from the PDB
MED-Ligand and MED-SuMo: computational fragment based drug design applications
The FBDD application gives results which are similar to docking as it returns poses in the binding site for molecules from a 2D molecular file. It has advantages as a reasonable number of molecules are usually found in the order of a few hundreds. The poses are relying on structural data and not on scoring functions. You don't have to worry about which scoring function to use and how well it performs. With MED-SuMo, it is as easy as using available structural information on ligand binding from the PDB.
The method doesn't rely on scoring functions, it is exploiting exhaustively the structural similarities between protein structures. The assumption is that two very similar protein environments are likely to bind the same fragment with the same relative pose.
Populate your binding site with rationally posed fragments
Hit Identification & Optimization
Focused library design
Follow this link for the training videos. They are aiming at supporting the current users in their drug discovery work and at showing the most relevant features to new users.