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 (biopteron - 4 CPUs - 16 Go RAM)
High quality (BEST mode) runs take 40 min: description of the surface with more triplets and up to 10,000 hits are collected
High speed (FAST mode) runs take 5 min: description of the surface with an optimized number of triplets and 1,000 hits are collected
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 | 40 |
| CytP450 3A4 | 2J0D / ERY | Sites 6Å | Best | 2J0D results | 40 |
| HIV1 Reverse transcriptase | 1RTI / HEF | Sites 6Å | Best | 1RTI results | 40 |
| HSP90 | 2VCI / 2GJ | Sites 6Å | Best | 2VCI results 1 results 2 results 3 |
40 |
| Phosphodiesterase | 1ROR / AMP | Sites 6Å | Best | 1ROR results | 40 |
| Phosphodiesterase | 1XP0 / VDN | Sites 6Å | Best | 1XP0 results | 40 |
| Protein kinase | 1UWH / BAX |
Sites 6Å | Best | 1UWH results | 40 |
| Protein kinase | 1FVV / 107 | Sites 6Å | Best | 1FVV results | 40 |
| Protein kinase | 1FVV / 107 |
Sites 6Å | Fast | 1FVV results | 20 |
| Protein phosphatase | 2VEW / IZ3 | Sites 6Å | Best | 2VEW results 1 results 2 results 3 results 4 |
40 |
| Serine protease | 1Y59 / TL1 |
Sites 6Å | Best | 1Y59 results | 40 |
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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