Year: 2017
Type: article
Abstract: 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 p K a values, and an improved web‐based visualization tool for viewing electrostatics.
Source: Protein Science
DOI: 10.1002/pro.3280
Authors: Elizabeth Jurrus, Dave Engel, Keith Star, Kyle Monson, Juan Brandi, Lisa E. Felberg, David H. Brookes, Leighton Wilson, Jiahui Chen, Karina Liles, Minju Chun, Peter Li, David W. Gohara, Todd Dolinsky, Robert Konecny, David R. Koes, Jens Erik Nielsen, Teresa Head‐Gordon, Weihua Geng, Robert Krasny, Guo‐Wei Wei, Michael J. Holst, J. Andrew McCammon, Nathan A. Baker
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: bronze
Funders: National Science Foundation, U.S. Department of Defense, U.S. Department of Energy, Battelle, National Institutes of Health, Office of Science, National Defense Science and Engineering Graduate, National Institute of General Medical Sciences, Division of Graduate Education, Division of Mathematical Sciences, Basic Energy Sciences, Pacific Northwest National Laboratory
Awards: G125460123, G1286236842, G1286251239, G138090931, APBS: Nanoscale Biomolecular Electrostatics Software, G1851334662, G1899721271, G2162194262, G2506945562, G2510423872, G2618837358, G2795275917, Collaborative Research: Boundary Integral Simulations for Solvent Effects in Protein Structure and Dynamics, G2988778103, G30714459, G3083819904, G3780241159, G391136020, G419881185, G42916606, G4501827968, G4725541805, G498139845, G5321382714, G5726405315, G613759197, G6450845587, G650090426, G6652958823, Theory of Biomolecular Diffusion, NATIONAL BIOMEDICAL COMPUTATION RESOURCE, G7665161096, G8135867528, G821644656, G969889393
OpenAlex ID: W2731784911