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- N A Baker, D Sept, S Joseph, M J Holst, J A McCammon
- Proceedings of the National Academy of Sciences…
- 2001

Evaluation of the electrostatic properties of biomolecules has become a standard practice in molecular biophysics. Foremost among the models used to elucidate the electrostatic potential is the Poisson-Boltzmann equation; however, existing methods for solving this equation have limited the scope of accurate electrostatic calculations to relatively small… (More)

- Todd J. Dolinsky, Jens E. Nielsen, James Andrew McCammon, Nathan A. Baker
- Nucleic Acids Research
- 2004

Continuum solvation models, such as Poisson-Boltzmann and Generalized Born methods, have become increasingly popular tools for investigating the influence of electrostatics on biomolecular structure, energetics and dynamics. However, the use of such methods requires accurate and complete structural data as well as force field parameters such as atomic… (More)

- Todd J. Dolinsky, Paul Czodrowski, +4 authors Nathan A. Baker
- Nucleic Acids Research
- 2007

Real-world observable physical and chemical characteristics are increasingly being calculated from the 3D structures of biomolecules. Methods for calculating pK(a) values, binding constants of ligands, and changes in protein stability are readily available, but often the limiting step in computational biology is the conversion of PDB structures into formats… (More)

- Dennis G. Thomas, Rohit V. Pappu, Nathan A. Baker
- Journal of Biomedical Informatics
- 2011

Data generated from cancer nanotechnology research are so diverse and large in volume that it is difficult to share and efficiently use them without informatics tools. In particular, ontologies that provide a unifying knowledge framework for annotating the data are required to facilitate the semantic integration, knowledge-based searching, unambiguous… (More)

- Zhan Chen, Nathan A. Baker, G. W. Wei
- J. Comput. Physics
- 2010

This paper presents a differential geometry based model for the analysis and computation of the equilibrium property of solvation. Differential geometry theory of surfaces is utilized to define and construct smooth interfaces with good stability and differentiability for use in characterizing the solvent-solute boundaries and in generating continuous… (More)

- Jason A Wagoner, Nathan A Baker
- Proceedings of the National Academy of Sciences…
- 2006

Continuum solvation models provide appealing alternatives to explicit solvent methods because of their ability to reproduce solvation effects while alleviating the need for expensive sampling. Our previous work has demonstrated that Poisson-Boltzmann methods are capable of faithfully reproducing polar explicit solvent forces for dilute protein systems;… (More)

- Michael J. Holst, Nathan A. Baker, Feng Wang
- Journal of Computational Chemistry
- 2000

This paper is the first of two papers on the adaptive multilevel finite element treatment of the nonlinear Poisson-Boltzmann equation (PBE), a nonlinear elliptic equation arising in biomolecular modeling. Fast and accurate numerical solution of the PBE is usually difficult to accomplish, due to presence of discontinuous coefficients, delta functions, three… (More)

- Nathan A Baker
- Current opinion in structural biology
- 2005

Recent developments in implicit solvent models may be compared in terms of accuracy and computational efficiency. Based on improvements in the accuracy of generalized Born methods and the speed of Poisson-Boltzmann solvers, it appears that the two techniques are converging to a point at which both will be suitable for simulating certain types of… (More)

- Samir Unni, Yong Huang, +5 authors Nathan A. Baker
- Journal of Computational Chemistry
- 2011

APBS and PDB2PQR are widely utilized free software packages for biomolecular electrostatics calculations. Using the Opal toolkit, we have developed a Web services framework for these software packages that enables the use of APBS and PDB2PQR by users who do not have local access to the necessary amount of computational capabilities. This not only increases… (More)

- David Sept, Nathan A Baker, J Andrew McCammon
- Protein science : a publication of the Protein…
- 2003

Microtubules are cylindrical polymers found in every eukaryotic cell. They have a unique helical structure that has implications at both the cellular level, in terms of the functions they perform, and at the multicellular level, such as determining the left-right symmetry in plants. Through the combination of an atomically detailed model for a microtubule… (More)