A software package to evaluate the electrostatic potential for very large biomolecular systems (millions of atoms). Solves the Poisson-Boltzmann equation using the Holst group PMG multigrid library and the FEtk finite element library, a highly scalable parallel solution method for elliptic problems.
An automated pipeline for the setup, execution, and analysis of Poisson-Boltzmann electrostatics calculations. Converts and optimizes PDB files into PQR files.
An ontology for nanotechnology applications in cancer therapeutics and diagnostics, developed by Dennis Thomas in collaboration with the Pappu lab.
A database which compares structure predictions from various prediction methods for various all genes in the S. cerevisiae genome.
A database which compares biomolecular electrostatics and other properties between structures in the Protein DataBank. Created by the Bajaj group based on collaborative work analyzing molecular electrostatics.
A software pacakge developed with Andreas Vitalis and J. Andrew McCammon which performs explicit ion simulations using primitive solvent models (i.e., implicit or dielectric continuum) and grand canonical Monte Carlo sampling.