Performances

Performances and examples on various binding sites

MED-SuMo is fast and user-friendly:

Can be applied to any protein family

Runs Site vs Site database take between 5 to 50 min with our evaluation server (bi-Xeon - 2 CPUs - 40cores - 256 GB RAM)

High quality (BEST mode) runs take 15 min: description of the surface with more triplets and up to 10,000 hits are collected (plus time to import data from server to GUI client)

High speed (FAST mode) runs take 5 min: description of the surface with an optimized number of triplets and 1,000 hits are collected (plus time to import data from server to GUI client)

Only true positives are observed in the top of the list according to MED-SuMo score

Interfamily hits are observed when false positives are becoming significant

False positives can be filtered out by advanced clustering features of the MED-SuMo GUI


Any 3D protein structure can be used as a query

Contact us to evaluate MED-SuMo on your target of interest

MED-SuMo runs can be as fast as 5 minutes towards the whole PDB, we report here results in the Fast and Best mode which are both giving very good quality results. Best mode is more exhaustive thanks to a more detailed description of the binding sites.

Query Query details (PDB / Ligand) Database Quality Screenshot of top ranked hits Approximate computational time (min)
Beta secretase 2VIJ / C44
Sites 6Å Best 2VIJ results 15
CytP450 3A4 2J0D / ERY Sites 6Å Best 2J0D results 15
HIV1 Reverse transcriptase 1RTI / HEF Sites 6Å Best 1RTI results 15
HSP90 2VCI / 2GJ Sites 6Å Best 2VCI results 1
results 2
results 3
15
Phosphodiesterase 1ROR / AMP Sites 6Å Best 1ROR results 15
Phosphodiesterase 1XP0 / VDN Sites 6Å Best 1XP0 results 15
Protein kinase 1UWH / BAX
Sites 6Å Best 1UWH results 15
Protein kinase 1FVV / 107 Sites 6Å Best 1FVV results 15
Protein kinase 1FVV / 107
Sites 6Å Fast 1FVV results 5
Protein phosphatase 2VEW / IZ3 Sites 6Å Best 2VEW results 1
results 2
results 3
results 4
15
Serine protease 1Y59 / TL1
Sites 6Å Best 1Y59 results 15


Tab 1: Example of MED-SuMo queries and hits for diverse targets. In the case of HSP90, a longer list of hits is reported to show that after many HSP90 hits, MED-SuMo finds interfamily hits, sharing the same Bergerat fold, whereas the sequence identity is known to be too low to infer binding site similarity. Results are obtained with the MED-SuMo GUI 1.1.38 on the 6.0 20-60 ST45 database (BEST) available on our evaluation server. (update on may 13th 2008: 50,822 PDB files ; 136,355 sites)

 

 


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