Tools for Computational Biology Research

gRINN: Get Residue Interaction eNergies and Networks

gRINN is a Graphical User as well as a Command-Line Interface (GUI/CLI) for efficient pairwise residue interaction energy computation from protein Molecular Dynamics (MD) simulation trajectories (generated by NAMD or GROMACS simulation software) and subsequent analysis/viewing of results. Features included are:

  • Pairwise interaction energy calculation of NAMD-generated MD simulation trajectories.
  • Custom residue selections
  • Multiple processor usage
  • Interaction energy correlation calculation
  • Construction of Protein Energy Networks that can be imported/analyses in external network analysis programs such as Cytoscape
  • Graphical User Interfaces for energy calculation and quick viewing of the results.
  • You can obtain the tool by clicking here.

    gRINN is not open-source software (for now). A manuscript proposal for gRINN is pending for approval! Once it is published, the repository containing the gRINN source-code will be made public.

    traj_analysis

    traj_analysis is a repository where I store small scripts for quick-and-easy MD simulation trajectory analysis.

    Miscallenous Stuff

    monitor-shutdown

    monitor-shutdown is a small package including two scripts for monitoring power outages. You probably do not need this if you don't experience frequent long-lasting power outages.