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Where to find protein data and run basic Molecular Dynamics simulation

Monday, July 11, 2016 at 08:47

โ€‹MDWeb is a handy tool

How to run a simulation: http://mmb.irbbarcelona.org/MDWeb//help.php?id=tutorialโ€‹

How to run an analysis: http://mmb.irbbarcelona.org/MDWeb//help.php?id=tutorialAnalysisโ€‹

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.

โ€‹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.