Improvements to the APBS biomolecular solvation software suite
| Autor: | Robert Konecny, David Ryan Koes, Nathan A. Baker, Jens Erik Nielsen, Dave Engel, Kyle E. Monson, Robert Krasny, Peter Li, Lisa E. Felberg, Karina Liles, Juan Brandi, David H. Brookes, J. Andrew McCammon, Guo-Wei Wei, Leighton Wilson, Minju Chun, Michael Holst, Elizabeth Jurrus, Todd J. Dolinsky, Teresa Head-Gordon, Weihua Geng, Keith T. Star, Jiahui Chen, David W. Gohara |
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| Rok vydání: | 2018 |
| Předmět: |
0301 basic medicine
Models Molecular titration Computer science Static Electricity Biophysics Bioengineering Biochemistry Computational science 03 medical and health sciences 0302 clinical medicine Software Models pK(a) pKa Other Information and Computing Sciences Molecular Biology Boundary element method Software suite Tools for Protein Science business.industry software Solvation Molecular Graph theory Biomolecules (q-bio.BM) Computation Theory and Mathematics Solver electrostatics Visualization 030104 developmental biology Networking and Information Technology R&D Quantitative Biology - Biomolecules Networking and Information Technology R&D (NITRD) FOS: Biological sciences Scalability Biochemistry and Cell Biology solvation business 030217 neurology & neurosurgery |
| Zdroj: | Protein science : a publication of the Protein Society, vol 27, iss 1 Jurrus, E; Engel, D; Star, K; Monson, K; Brandi, J; Felberg, LE; et al.(2018). Improvements to the APBS biomolecular solvation software suite. Protein Science, 27(1), 112-128. doi: 10.1002/pro.3280. UC San Diego: Retrieved from: http://www.escholarship.org/uc/item/3cg341d5 |
| Popis: | © 2017 The Protein Society 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 pKavalues, and an improved web-based visualization tool for viewing electrostatics. |
| Databáze: | OpenAIRE |
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