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Title: Improvements to the APBS biomolecular solvation software suite: Improvements to the APBS Software Suite

Abstract

The Adaptive Poisson-Boltzmann Solver (APBS) software was developed to solve the equations of continuum electrostatics for large biomolecular assemblages that has provided impact in the study of a broad range of chemical, biological, and biomedical applications. APBS addresses three key technology challenges for understanding solvation and electrostatics in biomedical applications: accurate and efficient models for biomolecular solvation and electrostatics, robust and scalable software for applying those theories to biomolecular systems, and mechanisms for sharing and analyzing biomolecular electrostatics data in the scientific community. To address new research applications and advancing computational capabilities, we have continually updated APBS and its suite of accompanying software since its release in 2001. In this manuscript, we discuss the models and capabilities that have recently been implemented within the APBS software package including: a Poisson-Boltzmann analytical and a semi-analytical solver, an optimized boundary element solver, a geometry-based geometric flow solvation model, a graph theory based algorithm for determining pKa values, and an improved web-based visualization tool for viewing electrostatics.

Authors:
 [1];  [1];  [1];  [1];  [1];  [2];  [2];  [3];  [4];  [1];  [1];  [1];  [5];  [6];  [7]; ORCiD logo [8];  [9];  [2];  [4];  [3] more »;  [10];  [7];  [7]; ORCiD logo [11] « less
  1. Pacific Northwest National Laboratory, Richland Washington
  2. University of California, Berkeley California
  3. University of Michigan, Ann Arbor Michigan
  4. Southern Methodist University, Dallas Texas
  5. St. Louis University, St. Louis Missouri
  6. FoodLogiQ, Durham North Carolina
  7. University of California San Diego, San Diego California
  8. University of Pittsburgh, Pittsburgh Pennsylvania
  9. Protein Engineering, Novozymes A/S, Copenhagen Denmark
  10. Michigan State University, East Lansing Michigan
  11. Pacific Northwest National Laboratory, Richland Washington; Brown University, Providence Rhode Island
Publication Date:
Research Org.:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1427908
Report Number(s):
PNNL-SA-127254
Journal ID: ISSN 0961-8368; 453040220
DOE Contract Number:  
AC05-76RL01830
Resource Type:
Journal Article
Journal Name:
Protein Science
Additional Journal Information:
Journal Volume: 27; Journal Issue: 1; Journal ID: ISSN 0961-8368
Publisher:
The Protein Society
Country of Publication:
United States
Language:
English
Subject:
continuum electrostatics; solvation and electrostatics; Biomedical applications; Poisson-Boltzmann

Citation Formats

Jurrus, Elizabeth, Engel, Dave, Star, Keith, Monson, Kyle, Brandi, Juan, Felberg, Lisa E., Brookes, David H., Wilson, Leighton, Chen, Jiahui, Liles, Karina, Chun, Minju, Li, Peter, Gohara, David W., Dolinsky, Todd, Konecny, Robert, Koes, David R., Nielsen, Jens Erik, Head-Gordon, Teresa, Geng, Weihua, Krasny, Robert, Wei, Guo-Wei, Holst, Michael J., McCammon, J. Andrew, and Baker, Nathan A. Improvements to the APBS biomolecular solvation software suite: Improvements to the APBS Software Suite. United States: N. p., 2017. Web. doi:10.1002/pro.3280.
Jurrus, Elizabeth, Engel, Dave, Star, Keith, Monson, Kyle, Brandi, Juan, Felberg, Lisa E., Brookes, David H., Wilson, Leighton, Chen, Jiahui, Liles, Karina, Chun, Minju, Li, Peter, Gohara, David W., Dolinsky, Todd, Konecny, Robert, Koes, David R., Nielsen, Jens Erik, Head-Gordon, Teresa, Geng, Weihua, Krasny, Robert, Wei, Guo-Wei, Holst, Michael J., McCammon, J. Andrew, & Baker, Nathan A. Improvements to the APBS biomolecular solvation software suite: Improvements to the APBS Software Suite. United States. doi:10.1002/pro.3280.
Jurrus, Elizabeth, Engel, Dave, Star, Keith, Monson, Kyle, Brandi, Juan, Felberg, Lisa E., Brookes, David H., Wilson, Leighton, Chen, Jiahui, Liles, Karina, Chun, Minju, Li, Peter, Gohara, David W., Dolinsky, Todd, Konecny, Robert, Koes, David R., Nielsen, Jens Erik, Head-Gordon, Teresa, Geng, Weihua, Krasny, Robert, Wei, Guo-Wei, Holst, Michael J., McCammon, J. Andrew, and Baker, Nathan A. Tue . "Improvements to the APBS biomolecular solvation software suite: Improvements to the APBS Software Suite". United States. doi:10.1002/pro.3280.
@article{osti_1427908,
title = {Improvements to the APBS biomolecular solvation software suite: Improvements to the APBS Software Suite},
author = {Jurrus, Elizabeth and Engel, Dave and Star, Keith and Monson, Kyle and Brandi, Juan and Felberg, Lisa E. and Brookes, David H. and Wilson, Leighton and Chen, Jiahui and Liles, Karina and Chun, Minju and Li, Peter and Gohara, David W. and Dolinsky, Todd and Konecny, Robert and Koes, David R. and Nielsen, Jens Erik and Head-Gordon, Teresa and Geng, Weihua and Krasny, Robert and Wei, Guo-Wei and Holst, Michael J. and McCammon, J. Andrew and Baker, Nathan A.},
abstractNote = {The Adaptive Poisson-Boltzmann Solver (APBS) software was developed to solve the equations of continuum electrostatics for large biomolecular assemblages that has provided impact in the study of a broad range of chemical, biological, and biomedical applications. APBS addresses three key technology challenges for understanding solvation and electrostatics in biomedical applications: accurate and efficient models for biomolecular solvation and electrostatics, robust and scalable software for applying those theories to biomolecular systems, and mechanisms for sharing and analyzing biomolecular electrostatics data in the scientific community. To address new research applications and advancing computational capabilities, we have continually updated APBS and its suite of accompanying software since its release in 2001. In this manuscript, we discuss the models and capabilities that have recently been implemented within the APBS software package including: a Poisson-Boltzmann analytical and a semi-analytical solver, an optimized boundary element solver, a geometry-based geometric flow solvation model, a graph theory based algorithm for determining pKa values, and an improved web-based visualization tool for viewing electrostatics.},
doi = {10.1002/pro.3280},
journal = {Protein Science},
issn = {0961-8368},
number = 1,
volume = 27,
place = {United States},
year = {2017},
month = {10}
}

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