PyPAICS

 PyPAICS is a PyMOL plug-in to represent IFIEs calculated by PAICS to protein structure on PyMOL. PyPAICS is constituted by following two modes: “All pair mode” and “Selected pair mode”.

Attention!

 Prior to run PyPAICS, all users have to run PAICS with referring to the following homepage (http://www.paics.net/index_e.html). Then the output file must be converted to csv file by RbAnalysisFMO developed by Takaki Tokiwa.

 

Introduction

  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), 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.
  PyPaics is a PyMOL plug-in to represent IFIEs calculated by PAICS to protein structure on PyMOL. PyPaics is constituted by following two modes: “All interaction mode” and “Ligand & protein mode”. Utilizing PyPaics, we can perform following things.

・(All pair mode) The IFIEs between user-defined residue and other residues forming top five of stable/repulsive interaction could be represented on protein structure in PyMOL.
・(Useful point of All pair mode) Following points could be estimated quantitatively: interaction energy which formed among protein domain interface, interaction network linking from active site to protein surface.

・(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.
・(Useful point of selected pair mode) Following points could be performed utilizing this mode: assignment of residues which are forming stable/unstable interaction with ligand. Remote interaction which formed with ligand.

  To run PyPAICS, users must install numpy in the system. In addition, users must obtain output file of PAICS by running it with following the procedure as shown in PAICS web site (http://www.paics.net/index_e.html).

  • Supporting operating system: Windows, Linux, Mac
  • Script language: Python 2.x (Not supporting Python 3.x)
  • Library: NumPy

Download

 PyPaics could be downloaded from following links.

 ・PyPAICS (Windows version)

・PyPAICS (Linux or Mac version)

 Test data of PyPaics could be downloaded from following links. The test_data were prepared by utilizing lectin structure (PDB ID: 2WQ4).

・ test_data (All interation mode, 2WQ4)

・test_data (Ligand & Protein mode, 2WQ4)

 Manual of PyPaics could be downloaded from following link.

・Manual of PyPAICS

[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