Software & other resources
APBS: Adaptive Poisson-Boltzmann Solver
http://www.poissonboltzmann.org/apbs
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.
PDB2PQR
http://www.poissonboltzmann.org/pdb2pqr
An automated pipeline for the setup, execution, and analysis of Poisson-Boltzmann electrostatics calculations. Converts and optimizes PDB files into PQR files.
Molecular Signatures server
http://cvcweb.ices.utexas.edu/ccv/projects/angstrom/pf/index.php
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.
ISIM
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.
NanoParticle Ontology
An ontology for nanotechnology applications in cancer therapeutics and diagnostics, developed by Dennis Thomas in collaboration with the Pappu lab.
caOBR
This is a middleware software project designed to
- Provide Bioportal Open Biomedical Repositories (OBR) access to caGrid resources
- Provide caGrid access to Bioportal Open Biomedical Repositories (OBR)
In both cases, this offers the ability to annotate and search a wide range of biomedical data resources with a large number of ontologies. Our initial development work has focused on the caNanoLab caGrid resource and the NanoParticle Ontology. The annotations provided by caOBR can currently be accessed through Bioportal (http://bioportal.bioontology.org/).
