Search, browse and superpose

 MED-SuMo: searching, browsing and superposing 3D macromolecules structure

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.

MED-SuMo is a software for searching, browsing and superposing 3D macromolecule structures:

   Protein kinases, serine proteases, phosphatases, aspartic proteases ...

   Non trivial superpositions of structures from different families or different superfamilies (Fig.1)

 

Fig.1: Example of non trivial protein superimpositions with MED-SuMo from left to right (orange and grey): (1) protein kinase b-raf (1UWH) and 5-methylthioribose kinase (2PYW) superimposed in the hinge region ; (2) protein kinase b-raf (1UWH) and scytalone dehydratase (5STD) superimposed in the allosteric pocket (3) serine protease FactorXa (1Y59) and serine protease Nocardiopsis alba Protease A (2OUA) superimposed in the P1 pocket (4) protein phosphatase PTP1B (2VEW) and phosphatase phytase (1U26) superimposed in the phosphate pocket.


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