The goal of this project is to enable the investigation of the salvation 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 energetic, salvation 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 salvation methods such as APBS requires accurate and complete structural data as well as force field parameters such as atomic charges and radii. Unfortunately, the limiting step in continuum electrostatics calculations is often the addition of missing atomic coordinates to molecular structures from the Protein Data Bank and the assignment of parameters to these structures. To address this problem, we have developed PDB2PQR. This server automates many of the common tasks of preparing structures for continuum salvation calculations as well as many other types of biomolecular structure modeling, analysis, and simulation. This automation allows any non-expert to convert PDB files into formats that can be used for more complex analyses. Like APBS, PDB2PQR is also distributed under an open source license to facilitate its use by biomedical researchers everywhere.

Public Health Relevance

An understanding of electrostatic interactions is essential for the study of the biomolecular-scale processes that are fundamental to understanding basic biological processes and undertaking the rational treatment of disease. Electrostatics plays an important role in all basic 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. The goal of this project is to enable the investigation of the salvation and electrostatic properties of macromolecules in biomedical re- search by supporting the maintenance and continued development of the open-source Adaptive Poisson-Boltzmann Solver and PDB2PQR software packages.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM069702-10
Application #
8232116
Study Section
Special Emphasis Panel (ZRG1-BST-Q (01))
Program Officer
Preusch, Peter C
Project Start
2004-01-15
Project End
2013-02-28
Budget Start
2012-03-01
Budget End
2013-02-28
Support Year
10
Fiscal Year
2012
Total Cost
$339,435
Indirect Cost
$140,562
Name
Battelle Pacific Northwest Laboratories
Department
Type
DUNS #
032987476
City
Richland
State
WA
Country
United States
Zip Code
99352
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:

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