%0 Generic %A D. Cooper, Christopher %A Bardhan, Jaydeep %A Barba, Lorena A. %D 2013 %T Binding energy of peptide-RNA complex with PyGBe and APBS %U https://figshare.com/articles/dataset/Binding_energy_of_peptide_RNA_complex_with_PyGBe_and_APBS/799704 %R 10.6084/m9.figshare.799704.v1 %2 https://ndownloader.figshare.com/files/1204835 %2 https://ndownloader.figshare.com/files/1204836 %2 https://ndownloader.figshare.com/files/1204837 %2 https://ndownloader.figshare.com/files/1204838 %2 https://ndownloader.figshare.com/files/1204839 %K PyGBe %K python %K cuda %K pycuda %K poisson-boltzmann %K GPU %K biomolecular electrostatics %K Molecular Physics %K Computational Biology %K Computational Physics %K Mechanical Engineering %K Biophysics %X

This file bundle includes data, figures and plotting scripts of solvation energy and binding energy calculations for peptide-RNA complex using PyGBe and APBS. Errors were calculated with respect to the corresponding extrapolated values (obtained from Richardson extrapolation).

This result is part of the paper:

—"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. Comput. Phys. Comm., 185(3):720–729 (March 2014). 10.1016/j.cpc.2013.10.028 // Preprint arXiv:1309.4018

 

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:

—Validation of the PyGBe code for Poisson-Boltzmann equation with boundary element methods. Christopher Cooper, Lorena A. Barba. figshare.
http://dx.doi.org/10.6084/m9.figshare.154331

 

Acknowledgement:
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.

 

%I figshare