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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

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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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