Browndye is a software package for performing Brownian dynamics simulations on large molecules.
Adaptive Poisson-Boltzmann Solver
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.
Interface to APBS
iAPBS is a C/Fortran interface to APBS which enables access to most of APBS capability from within any C or Fortran Code. In addition, an iAPBS/CHARMM module is available and an iAPBS/Amber module is in progress.
Grand Canonical Ensemble Monte Carlo Simulation of ions around biomolecules
ISIM is package that simulates the thermodynamic ensemble of ions around a macromolecule using a grand canonical monte carlo scheme and simple hard sphere ion models. It is meant to provide an alternative mechanism to mean field approaches to allow the calculation of ion distributions around a highly charged molecule using a simple model that takes into account ion-ion correlations and steric interactions. The original source was created in the McCammon group at UCSD (http://mccammon.ucsd.edu/isim/). The Java interface, SimTK ISIM, is a simple Java graphical user interface for running the program ISIM.
Autogrow Due in part to the increasing availability of crystallographic protein structures as well as rapid improvements in computer power, the past few decades have seen an explosion in the field of computer-based rational drug design. Several algorithms have been developed to identify or generate potential ligands in silico by optimizing the ligand-receptor hydrogen bond, electrostatic, and hydrophobic interactions. The novel drug-design algorithm described on this page, called AutoGrow (Java DOCK), uses fragment-based growing, docking, and evolutionary techniques. The original source was created in the McCammon group at UCSD (http://mccammon.ucsd.edu/~jdurrant/).