Improvements to the APBS biomolecular solvation software suite

被引：1443

作者：

Jurrus, Elizabeth ^{[1
]}

Engel, Dave ^{[1
]}

Star, Keith ^{[1
]}

Monson, Kyle ^{[1
]}

Brandi, Juan ^{[1
]}

Felberg, Lisa E. ^{[2
]}

Brookes, David H. ^{[2
]}

Wilson, Leighton ^{[3
]}

Chen, Jiahui ^{[4
]}

Liles, Karina ^{[1
]}

Chun, Minju ^{[1
]}

Li, Peter ^{[1
]}

Gohara, David W. ^{[5
]}

Dolinsky, Todd ^{[6
]}

Konecny, Robert ^{[7
]}

Koes, David R. ^{[8
]}

Nielsen, Jens Erik ^{[9
]}

Head-Gordon, Teresa ^{[2
]}

Geng, Weihua ^{[4
]}

Krasny, Robert ^{[3
]}

Wei, Guo-Wei ^{[10
]}

Holst, Michael J. ^{[7
]}

McCammon, J. Andrew ^{[7
]}

Baker, Nathan A. ^{[1
,11
]}

机构：

[1] Pacific Northwest Natl Lab, Richland, WA USA

[2] Univ Calif Berkeley, Berkeley, CA 94720 USA

[3] Univ Michigan, Ann Arbor, MI 48109 USA

[4] Southern Methodist Univ, Dallas, TX USA

[5] St Louis Univ, St Louis, MO 63103 USA

[6] FoodLogiQ, Durham, NC USA

[7] Univ Calif San Diego, San Diego, CA 92103 USA

[8] Univ Pittsburgh, Pittsburgh, PA USA

[9] Novozymes AS, Prot Engn, Copenhagen, Denmark

[10] Michigan State Univ, E Lansing, MI 48824 USA

[11] Brown Univ, Providence, RI 02912 USA

来源：

PROTEIN SCIENCE | 2018年 / 27卷 / 01期

基金：

美国国家科学基金会;

关键词：

electrostatics; software; solvation; titration; pK(a); POISSON-BOLTZMANN EQUATION; FINITE-ELEMENT SOLUTION; ACETYLCHOLINE DIFFUSION; MOLECULAR-DYNAMICS; PROTEIN STRUCTURES; BROWNIAN DYNAMICS; ELECTROSTATICS; SIMULATIONS; SOLVENT; ASSOCIATION;

D O I：

10.1002/pro.3280

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

The Adaptive Poisson-Boltzmann Solver (APBS) software was developed to solve the equations of continuum electrostatics for large biomolecular assemblages that have provided impact in the study of a broad range of chemical, biological, and biomedical applications. APBS addresses the 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 article, 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 pK(a) values, and an improved web-based visualization tool for viewing electrostatics.

引用

页码：112 / 128

页数：17

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