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Tools

by morris last modified 2012-01-23 14:54
Contributors: Sargis Dallakyan

Here is a list of tools that might be useful in docking.

See Also:

Format-Conversion Tools

  • Babel — Converts between many different kinds of molecular formats, including SYBYL mol2, PDB, InsightII car, and MDL SD formats. Available for UNIX, DOS and Mac OS.
  • hin2pdbq.py — Converts a HyperChem .hin-file to an AutoDock PDBQ-file. [Python script; needs "python", free from http://www.python.org/.]

Graphical Tools

  • Chimera — from UCSF, it 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. High-quality images and animations can be generated. Chimera includes complete documentation and several tutorials, and can be downloaded free of charge for academic, government, non-profit, and personal use."
  • Discovery Studio — from Accelrys, who claim it is the "most comprehensive suite of modeling and simulation solutions for drug discovery available".
  • gOpenMol — has, amongst other things, various AutoDock tools, including the ability to read and view trajectories from simulated annealing dockings. Written by Leif Laaksonen. Free.
  • MolMol — For displaying, analyzing, and manipulating the three-dimensional structure of biological macromolecules, with special emphasis on the study of protein or DNA structures determined by NMR. Imports: Residue Library, PDB, DIANA, DG, SYBYL(Mol2), XYZ. Exports: same as Imports, and... PostScript, MIF, EMF, TIFF, JPEG, PNG, BMP, POV-Ray, VRML.
  • MolScript — Display structures as images in various formats, or VRML
  • MolPOV — a Windows program to convert PDB files into POV-Ray input files.
  • PMV — from TSRI's MGL, it is a very extensible molecule viewer built from components written in Python.
  • PovChem — Non-graphical utility to convert PDB files into CPK, Ball and Stick, etc. POV-Ray input files. Runs under MSDOS, Irix(5.x), Mac (68k/PPC).
  • PyMOL — a popular, open-source, user-sponsored, molecular visualization system, that can easily produce ray-traced images and animations. PyMOL extends, and is extensible by, the Python programming language.
  • QuteMol — open source (GPL) molecule viewer that uses the GPU on your graphics card to create very clear and easy-to-read non-photorealistic renderings.
  • RasMol — can be used to view PDB files. Free. See also: RasMol Manual and Quick Reference Card.
  • Ribbons — from Mike Carson, it is great for creating non-photorealistic renderings of molecular surfaces and ribbons.
  • Swiss-PDB Viewer — can read in electron density maps, show sequence alignments, superimpose molecules, and easily create files forPOV-Ray, a free ray tracer. Runs on Apple Macintosh, iMacs and Power Macintoshes; & IBM PC clones.


Superimposing Molecules

  • ProFit — Protein least squares fitting.
  • Swiss-PDB Viewer — free, for Mac, PC and SGI; can be used to superimpose proteins (use "Iterative Magic Fit").


Lists of Software and Sites


Third Party Modifications to AutoDock*

*Note, we have not tested nor do we endorse this code.

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