PyGAMESS

PyGAMESS is a PyMOL plug-in to represent PIEs calculated by GAMESS to protein structure on PyMOL. PyGAMESS is constituted by following two modes: “All pair mode” and “Selected pair (PIEDA) mode”.


Attention!


Prior to run PyGAMESS, all users have to run GAMESS with referring to the following homepage (http://www.msg.ameslab.gov/gamess/). Then the output file must be converted to csv file by RbPaics developed by Takaki Tokiwa.

トピックス

  • Intermolecular interaction of protein/protein and protein/ligand affects to various their characters, such as protein stability, enzyme reactivity, enzyme inhibition and more. Estimation of the interaction quantitatively is important to design candidate of medicine and molecular probe. Here, fragment molecular orbital (FMO) is one of the method which can estimate the interaction energy by ab initio calculation. The calculated parameter, called inter fragment interaction energy (IFIE) or PIEs, could indicate the energy between ligand molecule and each amino acid residues in target protein, or residue-residue interaction in target proteins. The IFIEs can calculated several of already developed software, such as GAMESS and PAICS.   
  • PyGAMESS is a PyMOL plug-in to represent PIEs calculated by GAMESS to protein structure on PyMOL. PyGAMESS is constituted by following two modes: “All pair mode” and “Selected pair mode”. Utilizing PyGAMESSs, we can perform following things.
  • (All pair mode) The PIEs between user-defined residue and other residues forming top five of stable/repulsive interaction could be represented on protein structure in PyMOL.
  • (Selected pair mode) The intermolecular interaction could be represented on PyMOL between ligand and amino acid residues which located within the user defined distance. The interacting residues are colored with dependent on magnitude of IFIEs.
  • To run PyGAMESS, users must install numpy in the system. In addition, users must obtain output file of GAMESS by running it with following the procedure as shown in GAMESS web site (http://www.msg.ameslab.gov/gamess/).
  • Supporting operating system: Linux, Mac
  • Script language: Python 2.x (Not supporting Python 3.x)
  • Library: NumPy

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    [Reference]

    Takaki Tokiwa, Shogo Nakano et al., Development of an Analysis Toolkit, AnalysisFMO, to Visualize Interaction Energies Generated by Fragment Molecular Orbital Calculations, J. Chem. Inf. Model., DOI: 10.1021/acs.jcim.8b00649