Protein orientation near a charged surface using PyGBe and protein G B1 D4

This file bundle contains data, running script and final plot of the protein-orientation study for protein G B1 D4' near a charged surface. The running script invokes the bioelectrostatics solver (PyGBe) with the given input data, computes the orientation probability distribution and plots the final result. File set includes: —1 mesh, 2 bodies<br>—PQR file<br>—mesh-generation script for sensor surface<br>—input parameters and running script for mesher<br>—input file for PyGBe and running script<br>—CSV file of output (tilt, rotation, energy)<br>—Figure 11 of the paper and plotting script This result is part of an upcoming paper. Publication information will be updated at the time of submission with the arXiv pre-print number, and at the time of publication with the final citation. PyGBe solves biomolecular electrostatics problems using an implicit-solvent model (Poisson-Boltzmann) and it uses GPU hardware for fast execution. It is written in Python, PyCUDA and CUDA. More information about the PyGBe code in: —<em>"Validation of the PyGBe code for Poisson-Boltzmann equation with boundary element methods."</em> Christopher Cooper, Lorena A. Barba. figshare. http://dx.doi.org/10.6084/m9.figshare.154331 —"A biomolecular electrostatics solver using Python, GPUs and boundary elements that can handle solvent-filled cavities and Stern layers", Christopher D. Cooper, Jaydeep P. Bardhan, L. A. Barba. <em>Comput. Phys. Comm.</em>, <strong>185</strong>(3):720–729 (March 2014). 10.1016/j.cpc.2013.10.028 // Preprint arXiv:1309.4018 <strong>Acknowledgement:</strong> This research is made possible by support from the Office of Naval Research, Applied Computational Analysis Program, N00014-11-1-0356. LAB also acknowledges support from NSF CAREER award OCI-1149784.