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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Where to find protein data and run basic Molecular Dynamics simulation

​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

MDWeb is a handy tool

We-nmr: A worldwide e-Infrastructure for NMR and structural biology