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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)
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)
We describe what may be the most accurate approach currently available for the calculation of the pKas of ionizable groups in proteins. The accuracy is assessed by comparison of computed pKas with 60 measured pKas in a total of seven proteins. The overall root-mean-square error is 0.89 pKa units. Linear regression analysis of computed versus measured pKas(More)
Three-dimensional image reconstructions of large-scale protein aggregates are routinely determined by electron microscopy (EM). We combine low-resolution EM data with high-resolution structures of proteins determined by x-ray crystallography. A set of visualization and analysis procedures, termed the Situs package, has been developed to provide an efficient(More)
The dynamics of a folded globular protein (bovine pancreatic trypsin inhibitor) have been studied by solving the equations of motion for the atoms with an empirical potential energy function. The results provide the magnitude, correlations and decay of fluctuations about the average structure. These suggest that the protein interior is fluid-like in that(More)
UNLABELLED An automated procedure for the analysis of homologous protein structures has been developed. The method facilitates the characterization of internal conformational differences and inter-conformer relationships and provides a framework for the analysis of protein structural evolution. The method is implemented in bio3d, an R package for the(More)
Although the statistical thermodynamics of noncovalent binding has been considered in a number of theoretical papers, few methods of computing binding affinities are derived explicitly from this underlying theory. This has contributed to uncertainty and controversy in certain areas. This article therefore reviews and extends the connections of some(More)
Amphotericin B is a powerful but toxic antifungal antibiotic that is used to treat systemic infections. It forms ionic membrane channels in fungal cells. These antibiotic/sterol channels are responsible for the leakage of ions, which causes cell destruction. The detailed molecular properties and structure of amphotericin B channels are still unknown. In the(More)
The gating motion of the human nicotinic acetylcholine receptor (nAChR) alpha7 was investigated with normal mode analysis (NMA) of two homology models. The first model, referred to as model I, was built from both the Lymnaea stagnalis acetylcholine binding protein (AChBP) and the transmembrane (TM) domain of the Torpedo marmorata nAChR. The second model,(More)