Miscellaneous Tools
Red - Costware Green- Freeware/Shareware
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Program/Site |
Brief Description |
| 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. |
| GIMP | GIMP is an acronym for GNU Image Manipulation Program. Versions are available for Windows, Linux, Mac, and Unix. |
| GnuPlot | If you can write an equation, gnuplot can calculate it. I mean, functions to be plotted are expressed in a simple functional form, for example, f(x)=a*x+b, and they do not contain a complicated integration / differentiation which needs a numerical calculation. It can also be used for parameter-fitting to experimental data, namely a least-squares fitting. Gnuplot can solve not only linear least-squares problems but also non-linear ones. |
| GRID | Programme GRID is a computational procedure for determining energetically favourable binding sites on molecules of known structure. It may be used to study individual molecules such as drugs, molecular arrays such as membranes or crystals, and macromolecules such as proteins, nucleic acids, glycoproteins or polysaccharides. Several different molecules can be processed one after the other. |
| Imagemagick | ImageMagickTM 6.2.0 is a robust collection of tools and libraries to read, write, and manipulate an image in many image formats (over 90 major formats) including popular formats like TIFF, JPEG, PNG, PDF, PhotoCD, and GIF. |
| Inkscape | Inkscape is an Open Source vector graphics editor, with capabilities similar to Illustrator, Freehand, CorelDraw, or Xara X using the W3C standard Scalable Vector Graphics (SVG) file format. |
| mfold | Mfold web server for nucleic acid folding and hybridization prediction. |
| MMTSB | The MMTSB Tool Set is a collection of perl-based user-level utilities as well as programming libraries for multiscale protein structure modeling. Intended applications include protein structure prediction, loop modeling, structure refinement, and structure evaluation/scoring |
| MSMS | MSMS allows to compute very efficiently triangulations of Solvent Excluded Surfaces. |
| PDB2PQR | This server enables a user to convert PDB files into PQR files. PQR files are PDB files where the occupancy and B-factor columns have been replaced by per-atom charge and radius. |
| Plot Amber | Plotamber is a command line Perl script for an easy and automated plotting of properties derived from molecular dynamics or minimization calculations done with Amber. |
| PseudoViewer | An XML web service and web application program for visualizing RNA secondary structures with pseudoknots. It is claimed to be useful for visualizing large-scale RNA secondary structures with pseudoknots of any type. |
| RNAdraw | This program is suppose to be able to calculate secondary structure and then present in diagrammatic form, which can be editted. It runs on Win platforms. |
| RnaViz | RnaViz is a user-friendly, portable, GUI program for producing publication-quality secondary structure drawings of RNA molecules. Drawings can be created starting from DCSE alignment files if they incorporate structure information or from mfold ct files. The layout of a structure can be changed easily. Display of special structural elements such as pseudo-knots or unformatted areas is possible. Sequences can be automatically numbered, and several other types of labels can be used to annotate particular bases or areas. |
| Surfnet | The SURFNET program generates surfaces and void regions between surfaces from coordinate data supplied in a PDB file. It can compute van der Waals surfaces, gaps between molecules, clefts, cavities, and binding sites, 3D density distributions and sidechain-sidechain interactions, planes, paraboloids and boxes. |
| XRNA | XRNA is a Java based suite of tools for the creation, annotation and display of RNA secondary structure diagrams. |