MCCE (Multi-Conformation Continuum Electrostatics) is a biophysics simulation program combining continuum electrostatics and molecular mechanics to calculate pKa's of titratable amino acids. Developed by Professor Gunner and co-workers.
MoSuMo This is a program package designed to investigate and visualize the electrostatic potentials across molecular surfaces and the regions that correspond to binding sites. MoSuMo is developed in the Professor Dumontier's Lab.
VASCo VASCo is a program pipeline including a visualization tool to calculate and visualize annotated surfaces with special emphasis on surface contact regions and protein-protein interactions. Crystal contacts and biological contacts can be calculated based on surface points. Molecular properties such as electrostatic potential or hydrophobicity can be calculated and mapped on those surface points.
Developed by Professor Gerhard Thallinger
DelEnsembleElec A new VMD plugin that interfaces with DelPhi to provide ensemble-averaged electrostatic calculations using the Poisson-Boltzmann equation is presented. The general theory and context of this approach are discussed, and examples of the plugin interface and calculations are presented. This new tool is applied to systems of current biological interest, obtaining the ensemble-averaged electrostatic properties of the two major influenza virus glycoproteins, hemagglutinin and neuraminidase, from explicitly solvated all-atom molecular dynamics trajectories. The differences between the ensemble-averaged electrostatics and those obtained from a single structure are examined in detail for these examples, revealing how the plugin can be a powerful tool in facilitating the modeling of electrostatic interactions in biological systems.
Developed in Professor Rommie E. Amaro Lab.
Biskit is a python structural bioinformatics platform. Biskit contains a wrapper for Delphi and offers a small pipeline that automates the calculation of electrostatic free energies of binding for protein and DNA complexes: The input structure is protonated with the reduce program, chain breaks can be automatically detected and treated, Amber partial charges are assigned to every atom and compiled into a custom delphi charge file, delphi is run 6 times and binding energies are calculated from the result.
It was developed by Professor Raik Grünberg.
Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. Chimera provides DelPhiController, which is an interface to DelPhi allowing the user to choose the parameters of the calculations and to visualize the results.
Developed in Professor Thomas Ferrin lab.
Ascalaph is a general purpose molecular mechanics software with additional interfaces to external packages: DelPhi, MDynaMix, NWChem, CP2K and PC GAMESS/Firefly.
prmtop2pqr is a Python script allows you to convert an Amber (version 7 and higher), topology file (.prmtop) into a pqr format. This script takes as input the pdb of the system, the prmtop file, the output pqr file name and, optionally, a VMD-like atom selection string. To parse the pdb and apply the selection the ProDy package is used and must be previously installed. Developed by Sergio Decherchi, José. Colmenares and Walter Rocchia. ProDy is an excellent tool to manipulate MD trajectories and pdb files and can be dowloaded here.