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- Andrew T Fenley, John C Gordon, Alexey Onufriev
- The Journal of chemical physics
- 2008

Analytical approximations to fundamental equations of continuum electrostatics on simple shapes can lead to computationally inexpensive prescriptions for calculating electrostatic properties of realistic molecules. Here, we derive a closed-form analytical approximation to the Poisson equation for an arbitrary distribution of point charges and a spherical… (More)

- John C Gordon, Andrew T Fenley, Alexey Onufriev
- The Journal of chemical physics
- 2008

An ability to efficiently compute the electrostatic potential produced by molecular charge distributions under realistic solvation conditions is essential for a variety of applications. Here, the simple closed-form analytical approximation to the Poisson equation rigorously derived in Part I for idealized spherical geometry is tested on realistic shapes.… (More)

- Andrew T Fenley, David A Adams, Alexey V Onufriev
- Biophysical journal
- 2010

Presented here is a quantitative model of the wrapping and unwrapping of the DNA around the histone core of the nucleosome that suggests a mechanism by which this transition can be controlled: alteration of the charge state of the globular histone core. The mechanism is relevant to several classes of posttranslational modifications such as histone… (More)

- Ramu Anandakrishnan, Tom R W Scogland, Andrew T Fenley, John C Gordon, Wu-chun Feng, Alexey V Onufriev
- Journal of molecular graphics & modelling
- 2010

Tools that compute and visualize biomolecular electrostatic surface potential have been used extensively for studying biomolecular function. However, determining the surface potential for large biomolecules on a typical desktop computer can take days or longer using currently available tools and methods. Two commonly used techniques to speed-up these types… (More)

- Hari S. Muddana, Andrew T. Fenley, David L. Mobley, Michael K. Gilson
- Journal of Computer-Aided Molecular Design
- 2014

Prospective validation of methods for computing binding affinities can help assess their predictive power and thus set reasonable expectations for their performance in drug design applications. Supramolecular host-guest systems are excellent model systems for testing such affinity prediction methods, because their small size and limited conformational… (More)

- Alban R Pereira, Andrew J Kale, +6 authors William H Gerwick
- Chembiochem : a European journal of chemical…
- 2012

Two new peptidic proteasome inhibitors were isolated as trace components from a Curaçao collection of the marine cyanobacterium Symploca sp. Carmaphycin A (1) and carmaphycin B (2) feature a leucine-derived α,β-epoxyketone warhead directly connected to either methionine sulfoxide or methionine sulfone. Their structures were elucidated on the basis of… (More)

- Grigori Sigalov, Andrew Fenley, Alexey Onufriev
- The Journal of chemical physics
- 2006

The modeling and simulation of macromolecules in solution often benefits from fast analytical approximations for the electrostatic interactions. In our previous work [G. Sigalov et al., J. Chem. Phys. 122, 094511 (2005)], we proposed a method based on an approximate analytical solution of the linearized Poisson-Boltzmann equation for a sphere. In the… (More)

- Andrew T Fenley, Hari S Muddana, Michael K Gilson
- Proceedings of the National Academy of Sciences…
- 2012

Molecular dynamics simulations of unprecedented duration now can provide new insights into biomolecular mechanisms. Analysis of a 1-ms molecular dynamics simulation of the small protein bovine pancreatic trypsin inhibitor reveals that its main conformations have different thermodynamic profiles and that perturbation of a single geometric variable, such as a… (More)

- Abhishek Mukhopadhyay, Andrew T Fenley, Igor S Tolokh, Alexey V Onufriev
- The journal of physical chemistry. B
- 2012

Charge hydration asymmetry (CHA) manifests itself in the experimentally observed strong dependence of free energy of ion hydration on the sign of the ion charge. This asymmetry is not consistently accounted for by popular models of solvation; its magnitude varies greatly between the models. While it is clear that CHA is somehow related to charge… (More)

- Andrew T. Fenley, Niel M. Henriksen, Hari S. Muddana, Michael K. Gilson
- Journal of chemical theory and computation
- 2014

We used microsecond time scale molecular dynamics simulations to compute, at high precision, binding enthalpies for cucurbit[7]uril (CB7) with eight guests in aqueous solution. The results correlate well with experimental data from previously published isothermal titration calorimetry studies, and decomposition of the computed binding enthalpies by… (More)