| Package Name | PI | Package Description |
| APBS: Adaptive Poisson-Boltzmann Solver |
Baker |
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. |
| FORCE FIELD EXPLORER |
Ponder |
A Java-based molecular modeling program that serves as a graphical user interface (GUI) to the TINKER program package. Systems can be visualized using common representations such as wireframe, ball & stick, tubes and spacefilled models. |
| Gorgon |
Ju |
An interactive molecular modeling system specifically geared
towards cryo-EM and other low resolution structures of macromolecular
complexes. The long term objective of the tool is to be able to address to
every part of the molecular modeling pipeline starting from the initial
volumetric reconstruction of the complex all the way to the final
placement of each individual atom. |
| ISIM |
Baker |
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 |
Baker/Pappu |
An ontology for nanotechnology applications in cancer therapeutics and diagnostics, developed by Dennis Thomas in collaboration with the Pappu lab. |
| PDB2PQR |
Baker |
An automated pipeline for the setup, execution, and analysis of Poisson-Boltzmann electrostatics calculations. Converts and optimizes PDB files into PQR files. |
| PROPAK |
Ponder |
A program to attack the "inverse" protein folding problem via modeling of the side chain packing in proteins. Allows the user to redesign a portion of a known structure using a library of side chain rotamers |
| QSAR |
Ponder |
A program to derive QSAR models via regression analysis. The analysis can be performed by ordinary least squares (OLS), principal components (PCR) or partial least squares (PLS). |
| SLEUTH |
Ponder |
A small set of programs that allow creation of PDB file summaries and searching of a dataset extracted from the PDB for structural motifs. |
| TINKER |
Ponder |
A complete package for molecular mechanics, dynamics and modeling of molecules, especially biomacromolecules. TINKER has the ability to use any of several common parameter sets, such as Amber (ff94, ff96, ff98, ff99), CHARMM (19 and 27), Allinger MM (MM2-1991 and MM3-2000), OPLS (OPLS-UA, OPLS-AA and OPLS-AA/L), as well as our own AMOEBA polarizable atomic multipole force field. |
| Vocabulary Webpage Overlay |
Baker |
This is a simple tool designed to facilitate end-user and web-developer interaction with controlled vocabularies such as the Enterprise Vocabulary System (EVS) or various ontologies. |
