The goal of this project is to enable the investigation of the solvation and electrostatic properties of macromolecules in biomedical research by supporting the maintenance and continued development of the open-source Adaptive Poisson-Boltzmann Solver and PDB2PQR software packages. An understanding of electrostatic interactions is essential for the study of biomolecular processes. The structures of proteins and other biopolymers are being determined at an increasing rate through structural genomics and other efforts while specific linkages of these biopolymers in cellular pathways or supramolecular assemblages are being detected by genetic and proteomic studies. To integrate this information in physical models for drug discovery or other applications requires the ability to evaluate the energetic interactions within and between biopolymers. Among the various components of molecular energetics, solvation properties and electrostatic interactions are of special importance due to the long range of these interactions and the substantial charges of typical biopolymer components. APBS is a unique software package which solves the equations of continuum electrostatics for large biomolecular assemblages. This software was designed "from the ground up" using modern design principles to ensure its ability to interface with other computational packages and evolve as methods and applications change over time. The APBS code is accompanied by extensive documentation for both users and programmers and is supported by a variety of utilities for preparing calculations and analyzing results. Finally, the free, open-source APBS license ensures its accessibility to the entire biomedical community. The use of continuum solvation methods such as APBS requires accurate and complete structural data as well as force field parameters such as atomic charges and radii. PDB2PQR provides a software solution for such parameterization as well as biomolecular titration state assignment and visualization capability to support use by researchers with a wide range of expertise.

Public Health Relevance

Electrostatics plays an important role in all molecular-scale phenomena and therefore is integral to the analysis of biomolecular structure and interactions, including the study of health-related protein mutations and design of new molecular therapies. This project supports models for understanding electrostatics and solvation through the continued development of the open-source APBS and PDB2PQR software packages.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
Project #
Application #
Study Section
Biodata Management and Analysis Study Section (BDMA)
Program Officer
Preusch, Peter C
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
Battelle Pacific Northwest Laboratories
United States
Zip Code
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
Thomas, Dennis G; Gaheen, Sharon; Harper, Stacey L et al. (2013) ISA-TAB-Nano: a specification for sharing nanomaterial research data in spreadsheet-based format. BMC Biotechnol 13:2
Thomas, Dennis G; Chun, Jaehun; Chen, Zhan et al. (2013) Parameterization of a geometric flow implicit solvation model. J Comput Chem 34:687-95
Lee, Sun-Joo; Schlesinger, Paul H; Wickline, Samuel A et al. (2011) Interaction of melittin peptides with perfluorocarbon nanoemulsion particles. J Phys Chem B 115:15271-9
Unni, Samir; Huang, Yong; Hanson, Robert M et al. (2011) Web servers and services for electrostatics calculations with APBS and PDB2PQR. J Comput Chem 32:1488-91
Olsen, Brett N; Schlesinger, Paul H; Ory, Daniel S et al. (2011) 25-Hydroxycholesterol increases the availability of cholesterol in phospholipid membranes. Biophys J 100:948-56
Carstensen, Tommy; Farrell, Damien; Huang, Yong et al. (2011) On the development of protein pKa calculation algorithms. Proteins 79:3287-98
Alexov, Emil; Mehler, Ernest L; Baker, Nathan et al. (2011) Progress in the prediction of pKa values in proteins. Proteins 79:3260-75
Stone, John E; Gohara, David; Shi, Guochun (2010) OpenCL: A Parallel Programming Standard for Heterogeneous Computing Systems. Comput Sci Eng 12:66-72
Callenberg, Keith M; Choudhary, Om P; de Forest, Gabriel L et al. (2010) APBSmem: a graphical interface for electrostatic calculations at the membrane. PLoS One 5:

Showing the most recent 10 out of 26 publications