Abstract

The goal of this project is to continue to enable the investigation of the electrostatic properties of macromolecules for biomedical research by supporting the maintenance and continued development of the open-source Adaptive Poisson-Boltzmann Solver (APBS) software. Among the various inter- and intermolecular interactions in biomolecules, electrostatic energetics are of special importance due to their long range and the substantial charges of biopolymer components. APBS is a free, open-source software package designed to solve the equations of continuum electrostatics for large biomolecular assemblages using new highly-scalable parallel algorithms. This software was designed """"""""from the ground up"""""""" using modern software design methods to facilitate its modification and integration with other software packages. In order to ensure the continuing availability of APBS, we propose to ensure its suitability for both end-users and software developers in the biology community through continuing maintenance; to improve existing features based on new algorithms and user feedback; to incorporate new features based on the needs of the research community; and to expand the APBS user base by educating users, improving the efficiency and portability of the code, and facilitating interaction with other biomolecular software simulation packages.

  Funding Agency

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
1R01GM069702-01
Application #
6704346
Study Section
Special Emphasis Panel (ZRG1-SSS-H (91))
Program Officer
Wehrle, Janna P
Project Start
2004-01-15
Project End
2008-12-31
Budget Start
2004-01-15
Budget End
2004-12-31
Support Year
1
Fiscal Year
2004
Total Cost
$272,340
Indirect Cost

  Institution

Name
Washington University
Department
Biochemistry
Type
Schools of Medicine
DUNS #
068552207
City
Saint Louis
State
MO
Country
United States
Zip Code
63130

  Publications

Jurrus, Elizabeth; Engel, Dave; Star, Keith et al. (2018) Improvements to the APBS biomolecular solvation software suite. Protein Sci 27:112-128
Felberg, Lisa E; Brookes, David H; Yap, Eng-Hui et al. (2017) PB-AM: An open-source, fully analytical linear poisson-boltzmann solver. J Comput Chem 38:1275-1282
Gosink, Luke J; Overall, Christopher C; Reehl, Sarah M et al. (2017) Bayesian Model Averaging for Ensemble-Based Estimates of Solvation-Free Energies. J Phys Chem B 121:3458-3472
Purvine, Emilie; Monson, Kyle; Jurrus, Elizabeth et al. (2016) Energy Minimization of Discrete Protein Titration State Models Using Graph Theory. J Phys Chem B 120:8354-60
Vergara-Perez, Sandra; Marucho, Marcelo (2016) MPBEC, a Matlab Program for Biomolecular Electrostatic Calculations. Comput Phys Commun 198:179-194
Gunner, M R; Baker, N A (2016) Continuum Electrostatics Approaches to Calculating pKas and Ems in Proteins. Methods Enzymol 578:1-20
Pan, Wenxiao; Daily, Michael; Baker, Nathan A (2015) Numerical calculation of protein-ligand binding rates through solution of the Smoluchowski equation using smoothed particle hydrodynamics. BMC Biophys 8:7
Lei, H; Yang, X; Zheng, B et al. (2015) CONSTRUCTING SURROGATE MODELS OF COMPLEX SYSTEMS WITH ENHANCED SPARSITY: QUANTIFYING THE INFLUENCE OF CONFORMATIONAL UNCERTAINTY IN BIOMOLECULAR SOLVATION. Multiscale Model Simul 13:1327-1353
Gosink, Luke J; Hogan, Emilie A; Pulsipher, Trenton C et al. (2014) Bayesian model aggregation for ensemble-based estimates of protein pKa values. Proteins 82:354-63
Chakraborty, Sandeep; Rao, Basuthkar J; Baker, Nathan et al. (2013) Structural phylogeny by profile extraction and multiple superimposition using electrostatic congruence as a discriminator. Intrinsically Disord Proteins 1:

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