Working with MED-SuMo

Input

MED-SuMo uses as input a macromolecular structure database with up to hundreds of thousands structures:
  • the PDB (default)
  • in house curated database
  • models

Output

  • Ligand are aligned, shown in the graphical user interface and output as they are defined in the original PDB file.
  • In house curation of PDB ligands can be applied on the output of MED-SuMo.
  • MEDIT is providing by default an optional bond order and aromatic perception for PDB ligands.
  • Superposed ligand and/or proteins can be exported in PDB, SDF and Mol2 file format.

Find the most interesting hits with the MED-SuMo score

Working with MED-SuMo is easy and fast. Simply by clicking, superpositions of structures and fragments can be displayed in the 3D viewer. Hits are retreived and ranked in a spreadsheet according to the MED-SuMo score which takes into account chemical features and shape and is very efficient to identify the best hits:
  • Only true positives are found on the top of list (MED-SuMo score > 6.0)
  • Interfamily hits are found from MED-SuMo score 6.0 to 3.0
  • False positives have a drastically different signature than true positives and they can easily be filtered out

MED-SuMo server

  • Runs on linux systems
  • Takes advantage of the most recent hardware architectures: multicore processors and computer clusters
  • Command Line User Interface (CLUI) with LUA scripts
  • Is fully integrated into Scitegic Pipeline Pilot
  • MED-SuMo databases are easy to update from the PDB website


MED-SuMo graphical user interface GUI

  • Runs on Windows: XP, Vista,Seven, 8, 10
  • Runs on Mac with ParallelsTM
  • MED-SuMo server can be interfaced for MOE 2003 and Scitegic Pipeline Pilot 6.1.5

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