Electrostatics of nanosystems: Application to microtubules and the ribosome
- Nathan A. Baker, D. Sept, S. Joseph, M. Holst, J. Mccammon
- Physics, BiologyProceedings of the National Academy of Sciences…
- 21 August 2001
The application of numerical methods are presented to enable the trivially parallel solution of the Poisson-Boltzmann equation for supramolecular structures that are orders of magnitude larger in size.
PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations
- Todd J. Dolinsky, J. Nielsen, J. Mccammon, Nathan A. Baker
- Physics, ChemistryNucleic Acids Res.
- 1 July 2004
The PDB2PQR web service is intended to facilitate the setup and execution of Electrostatics calculations for both experts and non-experts and thereby broaden the accessibility to the biological community of continuum electrostatics analyses of biomolecular systems.
Brownian dynamics with hydrodynamic interactions
- D. Ermak, J. Mccammon
- Physics
- 15 August 1978
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 external…
Situs: A package for docking crystal structures into low-resolution maps from electron microscopy.
- W. Wriggers, R. Milligan, J. Mccammon
- ChemistryJournal of Structural Biology
- 1 April 1999
A set of visualization and analysis procedures, termed the Situs package, has been developed to provide an efficient and robust method for the localization of protein subunits in low-resolution data.
Molecular dynamics simulations of biomolecules
- M. Karplus, J. Mccammon
- Biology, ChemistryNature Structural Biology
- 1 September 2002
A brief description of the origin and early uses of biomolecular simulations is presented, some recent studies that illustrate the utility of such simulations are outlined and their ever-increasing potential for contributing to biology is discussed.
Improvements to the APBS biomolecular solvation software suite
- E. Jurrus, David Engel, Nathan A. Baker
- Computer ScienceProtein Science
- 30 June 2017
The models and capabilities that have recently been implemented within the APBS software package including a Poisson–Boltzmann analytical and a semi‐analytical solver, an optimized boundary element solvers, a geometry‐based geometric flow solvation model, a graph theory‐based algorithm for determining pKa values, and an improved web‐based visualization tool for viewing electrostatics are discussed.
Electrostatics and diffusion of molecules in solution: simulations with the University of Houston Brownian dynamics program
- J. Madura, J. Briggs, J. Mccammon
- Physics
- 2 September 1995
Prediction of pH-dependent properties of proteins.
- J. Antosiewicz, J. Mccammon, M. Gilson
- BiologyJournal of Molecular Biology
- 5 May 1994
It is suggested that the high protein dielectric constant improves the overall agreement with experiment because it accounts approximately for phenomena which tend to mitigate pKa shifts and which are not specifically included in the model.
Bio3d: an R package for the comparative analysis of protein structures
- B. Grant, Ana P. C. Rodrigues, K. M. ElSawy, J. Mccammon, L. Caves
- BiologyBioinform.
- 1 October 2006
UNLABELLED
An automated procedure for the analysis of homologous protein structures has been developed. The method facilitates the characterization of internal conformational differences and…
Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules.
- D. Hamelberg, J. Mongan, J. Mccammon
- Chemistry, BiologyJournal of Chemical Physics
- 8 June 2004
A robust bias potential function is proposed that can be used in an efficient accelerated molecular dynamics approach to simulate the transition of high energy barriers without any advance knowledge of the location of either the potential energy wells or saddle points, and is shown to samples the conformational space more efficiently than normal molecular dynamics simulations, and converges to the correct canonical distribution.
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