skip to main content
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

This content will become publicly available on November 24, 2020

Title: Visualizing biomolecular electrostatics in virtual reality with UnityMol‐APBS

Authors:
 [1];  [1];  [1];  [1];  [1];  [1];  [2]; ORCiD logo [2]; ORCiD logo [3]
  1. Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory Richland Washington
  2. Laboratoire de Biochimie ThéoriqueCNRS, Université de Paris Paris France, Institut de Biologie Physico‐Chimique‐Fondation Edmond de RothschildPSL Research University Paris France
  3. Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory Richland Washington, Division of Applied MathematicsBrown University Providence Rhode Island
Publication Date:
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22)
OSTI Identifier:
1575785
Grant/Contract Number:  
47319
Resource Type:
Publisher's Accepted Manuscript
Journal Name:
Protein Science
Additional Journal Information:
Journal Name: Protein Science; Journal ID: ISSN 0961-8368
Publisher:
Wiley Blackwell (John Wiley & Sons)
Country of Publication:
United Kingdom
Language:
English

Citation Formats

Laureanti, Joseph A., Brandi, Juan, Offor, Elvis, Engel, David, Rallo, Robert, Ginovska, Bojana, Martinez, Xavier, Baaden, Marc, and Baker, Nathan A. Visualizing biomolecular electrostatics in virtual reality with UnityMol‐APBS. United Kingdom: N. p., 2019. Web. doi:10.1002/pro.3773.
Laureanti, Joseph A., Brandi, Juan, Offor, Elvis, Engel, David, Rallo, Robert, Ginovska, Bojana, Martinez, Xavier, Baaden, Marc, & Baker, Nathan A. Visualizing biomolecular electrostatics in virtual reality with UnityMol‐APBS. United Kingdom. doi:10.1002/pro.3773.
Laureanti, Joseph A., Brandi, Juan, Offor, Elvis, Engel, David, Rallo, Robert, Ginovska, Bojana, Martinez, Xavier, Baaden, Marc, and Baker, Nathan A. Mon . "Visualizing biomolecular electrostatics in virtual reality with UnityMol‐APBS". United Kingdom. doi:10.1002/pro.3773.
@article{osti_1575785,
title = {Visualizing biomolecular electrostatics in virtual reality with UnityMol‐APBS},
author = {Laureanti, Joseph A. and Brandi, Juan and Offor, Elvis and Engel, David and Rallo, Robert and Ginovska, Bojana and Martinez, Xavier and Baaden, Marc and Baker, Nathan A.},
abstractNote = {},
doi = {10.1002/pro.3773},
journal = {Protein Science},
number = ,
volume = ,
place = {United Kingdom},
year = {2019},
month = {11}
}

Journal Article:
Free Publicly Available Full Text
This content will become publicly available on November 24, 2020
Publisher's Version of Record

Save / Share:

Works referenced in this record:

Improved Treatment of Ligands and Coupling Effects in Empirical Calculation and Rationalization of p K a Values
journal, June 2011

  • Søndergaard, Chresten R.; Olsson, Mats H. M.; Rostkowski, Michał
  • Journal of Chemical Theory and Computation, Vol. 7, Issue 7
  • DOI: 10.1021/ct200133y

Density‐functional thermochemistry. III. The role of exact exchange
journal, April 1993

  • Becke, Axel D.
  • The Journal of Chemical Physics, Vol. 98, Issue 7, p. 5648-5652
  • DOI: 10.1063/1.464913

Correlation consistent valence basis sets for use with the Stuttgart–Dresden–Bonn relativistic effective core potentials: The atoms Ga–Kr and In–Xe
journal, February 2001

  • Martin, Jan M. L.; Sundermann, Andreas
  • The Journal of Chemical Physics, Vol. 114, Issue 8
  • DOI: 10.1063/1.1337864

From Virtual Reality to Immersive Analytics in Bioinformatics
journal, June 2018

  • Sommer, Björn; Baaden, Marc; Krone, Michael
  • Journal of Integrative Bioinformatics, Vol. 15, Issue 2
  • DOI: 10.1515/jib-2018-0043

Electric Fields and Enzyme Catalysis
journal, June 2017


UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations
journal, December 1992

  • Rappe, A. K.; Casewit, C. J.; Colwell, K. S.
  • Journal of the American Chemical Society, Vol. 114, Issue 25, p. 10024-10035
  • DOI: 10.1021/ja00051a040

The Amber biomolecular simulation programs
journal, January 2005

  • Case, David A.; Cheatham, Thomas E.; Darden, Tom
  • Journal of Computational Chemistry, Vol. 26, Issue 16
  • DOI: 10.1002/jcc.20290

UCSF ChimeraX: Meeting modern challenges in visualization and analysis: UCSF ChimeraX Visualization System
journal, September 2017

  • Goddard, Thomas D.; Huang, Conrad C.; Meng, Elaine C.
  • Protein Science, Vol. 27, Issue 1
  • DOI: 10.1002/pro.3235

A complete basis set model chemistry. I. The total energies of closed‐shell atoms and hydrides of the first‐row elements
journal, August 1988

  • Petersson, G. A.; Bennett, Andrew; Tensfeldt, Thomas G.
  • The Journal of Chemical Physics, Vol. 89, Issue 4
  • DOI: 10.1063/1.455064

Application of RESP charges to calculate conformational energies, hydrogen bond energies, and free energies of solvation
journal, October 1993

  • Cornell, Wendy D.; Cieplak, Piotr; Bayly, Christopher I.
  • Journal of the American Chemical Society, Vol. 115, Issue 21
  • DOI: 10.1021/ja00074a030

g_mmpbsa —A GROMACS Tool for High-Throughput MM-PBSA Calculations
journal, June 2014

  • Kumari, Rashmi; Kumar, Rajendra; Lynn, Andrew
  • Journal of Chemical Information and Modeling, Vol. 54, Issue 7
  • DOI: 10.1021/ci500020m

A complete basis set model chemistry. II. Open‐shell systems and the total energies of the first‐row atoms
journal, May 1991

  • Petersson, G. A.; Al‐Laham, Mohammad A.
  • The Journal of Chemical Physics, Vol. 94, Issue 9
  • DOI: 10.1063/1.460447

Improvements to the APBS biomolecular solvation software suite: Improvements to the APBS Software Suite
journal, October 2017

  • Jurrus, Elizabeth; Engel, Dave; Star, Keith
  • Protein Science, Vol. 27, Issue 1
  • DOI: 10.1002/pro.3280

Acetylcholinesterase: enzyme structure, reaction dynamics, and virtual transition states
journal, October 1987


Interactive molecular dynamics in virtual reality from quantum chemistry to drug binding: An open-source multi-person framework
journal, June 2019

  • O’Connor, Michael B.; Bennie, Simon J.; Deeks, Helen M.
  • The Journal of Chemical Physics, Vol. 150, Issue 22
  • DOI: 10.1063/1.5092590

PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations
journal, July 2004

  • Dolinsky, T. J.; Nielsen, J. E.; McCammon, J. A.
  • Nucleic Acids Research, Vol. 32, Issue Web Server, p. W665-W667
  • DOI: 10.1093/nar/gkh381

PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations
journal, May 2007

  • Dolinsky, T. J.; Czodrowski, P.; Li, H.
  • Nucleic Acids Research, Vol. 35, Issue Web Server
  • DOI: 10.1093/nar/gkm276

Development and testing of a general amber force field
journal, January 2004

  • Wang, Junmei; Wolf, Romain M.; Caldwell, James W.
  • Journal of Computational Chemistry, Vol. 25, Issue 9
  • DOI: 10.1002/jcc.20035

Electrostatic decoupling of periodic images of plane‐wave‐expanded densities and derived atomic point charges
journal, November 1995

  • Blöchl, P. E.
  • The Journal of Chemical Physics, Vol. 103, Issue 17
  • DOI: 10.1063/1.470314

NWChem: A comprehensive and scalable open-source solution for large scale molecular simulations
journal, September 2010

  • Valiev, M.; Bylaska, E. J.; Govind, N.
  • Computer Physics Communications, Vol. 181, Issue 9, p. 1477-1489
  • DOI: 10.1016/j.cpc.2010.04.018

UCSF Chimera?A visualization system for exploratory research and analysis
journal, January 2004

  • Pettersen, Eric F.; Goddard, Thomas D.; Huang, Conrad C.
  • Journal of Computational Chemistry, Vol. 25, Issue 13
  • DOI: 10.1002/jcc.20084

Ab Initio Calculation of Vibrational Absorption and Circular Dichroism Spectra Using Density Functional Force Fields
journal, November 1994

  • Stephens, P. J.; Devlin, F. J.; Chabalowski, C. F.
  • The Journal of Physical Chemistry, Vol. 98, Issue 45, p. 11623-11627
  • DOI: 10.1021/j100096a001

VMD: Visual molecular dynamics
journal, February 1996


The Poisson–Boltzmann equation and its application to polyelectrolytes
journal, June 1979

  • Fixman, Marshall
  • The Journal of Chemical Physics, Vol. 70, Issue 11
  • DOI: 10.1063/1.437340

Protein Scaffold Activates Catalytic CO 2 Hydrogenation by a Rhodium Bis(diphosphine) Complex
journal, November 2018

  • Laureanti, Joseph A.; Buchko, Garry W.; Katipamula, Sriram
  • ACS Catalysis, Vol. 9, Issue 1
  • DOI: 10.1021/acscatal.8b02615