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Protein folding and association: Insights from the interfacial and thermodynamic properties of hydrocarbons
We demonstrate in this work that the surface tension, water‐organic solvent, transfer‐free energies and the thermodynamics of melting of linear alkanes provide fundamental insights into the nonpolar…
Accurate Calculation of Hydration Free Energies Using Macroscopic Solvent Models
A method and parametrization scheme which allow fast and accurate calculations of hydration free energies are described. The solute is treated as a polarizable cavity of a shape defined by the…
A hierarchical approach to all‐atom protein loop prediction
The overall results are the best reported to date, and the combination of an accurate all‐atom energy function, efficient methods for loop buildup and side‐chain optimization, and, especially for the longer loops, the hierarchical refinement protocol is attributed.
Classical electrostatics in biology and chemistry.
A major revival in the use of classical electrostatics as an approach to the study of charged and polar molecules in aqueous solution has been made possible through the development of fast numerical…
A rapid finite difference algorithm, utilizing successive over‐relaxation to solve the Poisson–Boltzmann equation
An efficient algorithm is presented for the numerical solution of the Poisson–Boltzmann equation by the finite difference method of successive over‐relaxation, reducing the required computing time by between one and two orders of magnitude.
The role of DNA shape in protein-DNA recognition
These findings indicate that the ability to detect local variations in DNA shape and electrostatic potential is a general mechanism that enables proteins to use information in the minor groove, which otherwise offers few opportunities for the formation of base-specific hydrogen bonds, to achieve DNA-binding specificity.
Origins of specificity in protein-DNA recognition.
- R. Rohs, Xiangshu Jin, S. West, R. Joshi, B. Honig, R. Mann
- Biology, ChemistryAnnual review of biochemistry
- 9 June 2010
This review provides a revised view of protein-DNA interactions that emphasizes the importance of the three-dimensional structures of both macromolecules and argues that individual DNA-binding proteins combine multiple readout mechanisms to achieve DNA- binding specificity.
On the role of the crystal environment in determining protein side-chain conformations.
Electrostatic interactions in macromolecules: theory and applications.
This presentation discusses the construction of the Poisson-Boltzmann Equation, and some of the methods used to achieve this result.
Calculating the electrostatic potential of molecules in solution: Method and error assessment
We present a numerical method for calculating the electrostatic potential of molecules in solution, using the linearized Poisson‐Boltzmann equation. The emphasis in this work is on applications to…