Graphical User Interface for MOSAICS as a PyMOL plugin — PymoSAICS

MOSAICS is suite of sampling methods for molecular simulations of motion of nucleic acid and protein structures. It’s applicability has been demonstrated in simulating large ensembles of nucleic acids (Sim 2012, Minary 2014) and proteins.

Starting with a protein/dna/rna structure you would like to examine, the basic modus operandi of MOSAICS is divided into three parts:

  • Pick your energy function or a statistical/empirical potentials (e.g. empirical Amber or CHARMM)
  • Pick your sampling methodology — e.g. parallel tempering
  • Details of simulation: solvent (implicit?), degrees of freedom (cartesian, torsional?) etc.

The energy function defines the energy surface with respect to your degrees of freedom (DoFs) and the sampling methodology is supposed to explore the conformational space along DoFs.

One of the main fortes of MOSAICS lies in the ability of defining hierarchichal natural moves. Defining regions of collective motion introduces experimental knowledge and intuition into the simulations, greatly accelerating sampling. Ability to define such regions  was one of the main reasons to start the development of the graphical user interface (GUI) for MOSAICS — preliminary version can be seen in the Figure below.

WorkshopPoster

Overview of PymoSAICS in its current form.

Since we are developing the GUI as a plugin for Pymol, we called it PymoSAICS. The initial focus of the project is on nucleic acids due to our interests in the structural effects of epigenetic modifications. As demonstrated in the Figure above, the GUI is divided into three main panels:

  • Current run — prepare a simulation
  • Simulation Manager — manage previous runs, import, export protocols
  • Help — That’s just a link to our website!

Users can upload their favorite structure via PymoSAICS or Pymol and play with the available parameters. The GUI is also an ongoing effort to streamline the available protocols in MOSAICS to shield the user from the many parameters that are available but perhaps not relevant to the simulation at hand.

We are currently starting beta tests of the application which (if you don’t mind not getting any support just yet) is available here, Therefore, if you are interested in becoming a tester please let me know, and you will receive a version around Easter (April-ish)! Contact me via konrad.krawczyk at dtc.ox.ac.uk

 

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