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 > 8.0)
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
Interfaces
MED-SuMo is a user friendly client/server software.
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
Can be administrated by a web interface (MED-Manager)
Is fully integrated into Scitegic Pipeline Pilot
MED-SuMo databases are easy to update from the PDB website
MED-SuMo GUI
Runs on Windows: 2000, server 2003, XP and Vista
Runs on Mac with ParallelsTM
MED-SuMo server can be interfaced for MOE 2003 and Scitegic Pipeline Pilot 6.1.5
Printable Page
