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| APBS | 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. |
| ARMS | Spatial Alignment with the RMS (Root Mean Square) method. ARMS reads the cartesian coordinates of two molecules, then optimally rotates and translates the molecule 2 onto the molecule 1. A pairwise correspondence between two equal length ranges of atoms is input. The maximal common 3D motif is computed after alignment, with the SDM algorithm. |
| ASV | ASV reads the cartesian coordinates of the molecule and the van der Waals radii of the atoms, then performs both Monte-Carlo and analytical calculation of the van der Waals surface and volume. |
| CCP4 | The CCP4 program suite is a collection of disparate programs covering most of the computations required for macromolecular crystallography. |
| CSR | CSR is for Maximal Common 3D Substructure Searching. The programs is web based. |
| CURVES | Curves is an algorithm for calculating a helical parameter description for any irregular nucleic acid segment with respect to an optimal, global helical axis. |
| DOG | DOG reads the cartesian coordinates of two molecules, then translates
and rotates the molecule 2 for docking with the molecule 1. A pairwise correspondence between two equal length ranges of atoms is
input. When each of the two molecules is a single nucleotidic strand in
PDB/NDB format, the pairwise correspondence is defined from the atom-pairs enabling potential hydrogen bonds. The two input molecules should be concatenated into a single file prior execution. |
| GAP | GAP programs can be used to analyse three-dimensional structure ensembles, specifically with regard to statistical geometric properties. A first set of programs can be used to analyze restraint violations and internal coordinates (distances and torsion angles) in a single ensemble (sometimes called a structure 'family'). A subset of the analysis programs (some very new or recently updated) can be used to compare two or more different structure ensembles. |
| MeltDNA | A program for prediction of DNA duplex stability and thermodynamics. |
| MIPSIM | MIPSim is a computational system for the automatic exploration of biomolecular similarities on the basis of molecular interaction potentials. MIPSim can be used as a standalone program for the automatic exploration of biomolecular similarities but it is specially powerful when interfacing to other well-known external programs including GAMESS (quantum chemistry), GRID (molecular potential evaluator), PLS (partial least squares calc. needed for 3d-QSAR), GOLPE (3D-QSAR), GOPENMOL (visualization). |
| PlotAmber | This is a program to pull out various pieces of information from the Amber md.out file and reformat them for a suitable plotting program such as xmgr (aka grace). |