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Electrostatics of nanosystems: Application to microtubules and the ribosome
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 theExpand
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PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations
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,Expand
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Brownian dynamics with hydrodynamic interactions
A method for simulating the Brownian dynamics of N particles with the inclusion of hydrodynamic interactions is described. The particles may also be subject to the usual interparticle or externalExpand
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Situs: A package for docking crystal structures into low-resolution maps from electron microscopy.
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 ofExpand
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Molecular dynamics simulations of biomolecules
Molecular dynamics simulations are important tools for understanding the physical basis of the structure and function of biological macromolecules. The early view of proteins as relatively rigidExpand
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Prediction of pH-dependent properties of proteins.
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 60Expand
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The statistical-thermodynamic basis for computation of binding affinities: a critical review.
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 thisExpand
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Electrostatics and diffusion of molecules in solution : simulations with the University of Houston Brownian Dynamics program
Abstract Brownian dynamics simulations are not new, but typically progrmas have been written for specific systems. In this paper, we describe a general-purpose Brownian dynamics program that has beenExpand
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Dynamics of folded proteins
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. TheExpand
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The determinants of pKas in proteins.
Although validation studies show that theoretical models for predicting the pKas of ionizable groups in proteins are increasingly accurate, a number of important questions remain: (1) What factorsExpand
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