USPA Workshop - Electrostatics Calculations

review

The first CCPB USPA Specialised Training Workshop on the topic Electrostatics Calculations was held in the Department of Biology at the University of York on 9th January 2009.

The workshop was run by Nathan Baker (Washington University in St Louis) and Kaihsu Tai (University of Oxford), who guided participants through the use of APBS software. APBS is a software package for the numerical solution of the Poisson-Boltzmann equation (PBE), one of the most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media. Continuum electrostatics plays an important role in several areas of biomolecular simulation, including:

  * simulation of diffusional processes to determine ligand-protein and protein-protein binding kinetics,
  * implicit solvent molecular dynamics of biomolecules,
  * solvation and binding energy calculations to determine ligand-protein and protein-protein equilibrium binding constants and aid in rational drug design,
  * and biomolecular titration studies.

APBS was designed to efficiently evaluate electrostatic properties for such simulations for a wide range of length scales to enable the investigation of molecules with tens to millions of atoms.

downloads

All the workshop materials can be downloaded from:
http://cardon.wustl.edu/MediaWiki/index.php/CCPB_workshop_tutorials
including all presentations and tutorials. If you need to download the APBS software, this can be downloaded from:
http://apbs.sourceforge.net/.