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Where to find protein data and run basic Molecular Dynamics simulation
Monday, July 11, 2016 at 08:47
MDWeb
is a handy tool
How to run a simulation:
http://mmb.irbbarcelona.org/MDWeb//help.php?id=tutorial
How to run an analysis:
http://mmb.irbbarcelona.org/MDWeb//help.php?id=tutorialAnalysis
Get a structure file of the protein you wanna study
Some webtools requires an actual file to be uploaded for processing.
Download the structure file of the protein you want to study from the
Protein Data Bank (PDB)
. I'm using the
spider toxin
here.
We-nmr
: A worldwide e-Infrastructure for NMR and structural biology
They provide many tools:
3D-DART
AMBER
CcpNmr Analysis
CcpNmr FormatConverter
CING
CNS
CS-ROSETTA
CYANA
FANDAS
HADDOCK
GROMACS
MARS
TALOS+
UNIO
XPLOR-NIH
We can use
the GROMACS web server
. Tutorial can be found
here
.
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Contents
MDWeb is a handy tool
Get a structure file of the protein you wanna study
We-nmr: A worldwide e-Infrastructure for NMR and structural biology