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[PARENTDIR] Parent Directory - [DIR] AutoDock_Vina_manual_files/ 2020-10-02 17:16 - [   ] 2012_ADTtut.pdf 2020-10-02 17:15 953K Digital document (Acrobat) [TXT] about.txt 2020-10-02 17:15 3.7K Text, ASCII format [TXT] adrese.txt 2020-10-02 17:15 229 Addresses, URL [   ] AutoDock4.2.6_UserGuide.pdf 2020-10-02 17:15 2.6M Digital document (Acrobat) [   ] AutoDock4.2_UserGuide.pdf 2020-10-02 17:15 3.2M Digital document (Acrobat) [   ] autodock_vina_1_1_2.tgz 2020-10-02 17:16 66K Compressed archive [   ] autodock_vina_1_1_2_win32.msi 2020-10-02 17:16 500K MS Installation package [TXT] AutoDock_Vina_manual.htm 2020-10-02 17:16 43K Text, HTML format [   ] autodocksuite-4.2.6-examples.tar.gz 2020-10-02 17:15 11M Compressed archive [   ] autodocksuite-4.2.6-src.tar.gz 2020-10-02 17:16 34M Compressed archive [   ] autodocksuite-4.2.6.i86Windows.exe 2020-10-02 17:16 564K Executable binary [   ] doc_AutoDockTools_1.4.3.tar.gz 2019-01-24 20:53 2.0M Compressed archive [   ] doc_DejaVu_1.4.3.tar.gz 2019-01-24 20:53 1.0M Compressed archive [   ] doc_Pmv_1.4.3.tar.gz 2019-01-24 20:53 4.4M Compressed archive [   ] doc_Vision_1.4.6.tar.gz 2019-01-24 20:53 14M Compressed archive [   ] doc_Vision_NBCR_SI08.tar.gz 2019-01-24 20:53 20M Compressed archive [   ] mgltools_i86Darwin9_1.5.6.dmg 2019-01-24 20:53 64M Disk Image File [   ] mgltools_i86Linux2_1.5.6.tar.gz 2019-01-24 20:53 69M Compressed archive [   ] mgltools_Linux-x86_1.5.6_Install 2019-01-24 20:53 70M [   ] mgltools_Linux-x86_64_1.5.6_Install 2019-01-24 20:53 69M [   ] mgltools_source_1.5.6.tar.gz 2020-10-02 17:16 38M Compressed archive [   ] 2019-01-24 20:53 51M Compressed archive [   ] mgltools_win32_1.5.6_Setup.exe 2019-01-24 20:53 71M Executable binary [   ] mgltools_win32_1.5.7_Setup.exe 2020-10-02 17:16 80M Executable binary [   ] mgltools_x86_64Linux2_1.5.6.tar.gz 2019-01-24 20:53 68M Compressed archive [   ] mgltools_x86_64Linux2_1.5.7.tar_.gz 2020-10-02 17:16 107M Compressed archive [   ] msms_i86_64Linux2_2.6.1.tar.gz 2019-01-24 20:53 579K Compressed archive [   ] msms_i86Linux2_2.6.1.tar.gz 2019-01-24 20:53 110K Compressed archive [   ] msms_MacOSX_2.6.1.tar.gz 2019-01-24 20:53 222K Compressed archive [   ] 2019-01-24 20:53 157K Compressed archive [   ] PmvTut1page-1.pdf 2020-10-02 17:16 45M Digital document (Acrobat) [   ] Tests_AutoDockTools_1.4.5.tar.gz 2019-01-24 20:53 14M Compressed archive [   ] Tests_DejaVu_1.4.3.tar.gz 2019-01-24 20:53 44K Compressed archive [   ] Tests_Pmv_1.5.0.tar.gz 2019-01-24 20:54 9.0M Compressed archive [   ] Tests_Vision_1.4.3.tar.gz 2019-01-24 20:53 23K Compressed archive [   ] tutorial.tar.gz 2020-10-02 17:16 5.9M Compressed archive [   ] UsingAutoDock4WithADT.ppt.Handouts3pp.v3.pdf 2020-10-02 17:16 3.9M Digital document (Acrobat) [   ] VisionTut1Page.pdf 2020-10-02 17:16 15M Digital document (Acrobat)

Unless otherwise stated, packages that do not specify a license are released 
under the MOZILLA Open Source License. Check the licenses!

Thew MGLTools software suite was developed in the Sanner lab at the Center for 
Computational Structural Biology (CCRB) formerly known as the Molecular 
Graphics Laboratory (MGL) of The Scripps Research Institute for visualization 
and analysis of molecular structures. Navigation portlet on the left has links 
to downloads, screenshots, documentation section of this website where you can 
find more information about MGLTools. MGLTools comprises:

    the Python Molecular Viewer (PMV), a general purpose molecular viewer
    AutoDockTools (ADT) a set of PMV commands specifically developed to 
       support AutoDock users
    Vision, a visual programing environment.

MSMS - binaries of the MSMS C library.
This allows you to run msms as a standalone application. A wrapped version of
the library comes with MGLTools.

The MGLTools uses the MSLIB package to compute molecular surfaces. 


AutoDock 4 is free and is available under the GNU General Public License.

AutoDock is a Command-line interface suite of automated docking tools. It 
is designed to predict how small molecules, such as substrates or drug 
candidates, bind to a receptor of known 3D structure.

Current distributions of AutoDock consist of two generations of software: 
AutoDock 4 and AutoDock Vina.

AutoDock 4 actually consists of two main programs: autodock performs the 
docking of the ligand to a set of grids describing the target protein; 
autogrid pre-calculates these grids.

In addition to using them for docking, the atomic affinity grids can be 
visualised. This can help, for example, to guide organic synthetic chemists 
design better binders.

AutoDock Vina does not require choosing atom types and pre-calculating grid 
maps for them. Instead, it calculates the grids internally, for the atom 
types that are needed, and it does this virtually instantly.

We have also developed a graphical user interface called AutoDockTools, or 
ADT for short, which amongst other things helps to set up which bonds will 
treated as rotatable in the ligand and to analyze dockings.

AutoDock Vina

AutoDock Vina is released under a very permissive Apache license,
with few restrictions on commercial or non-commercial use, or on
the derivative works

AutoDock Vina is an open-source program for doing molecular docking. It was 
designed and implemented by Dr. Oleg Trott in the Molecular Graphics Lab at 
The Scripps Research Institute.


AutoDockTools, or ADT, is the free GUI for AutoDock developed by the same 
laboratory that develops AutoDock. You can use it to set up, run and 
analyze AutoDock dockings and isocontour AutoGrid affinity maps, as well 
as compute molecular surfaces, display secondary structure ribbons, 
compute hydrogen-bonds, and do many more useful things.

AutoDockTools, or ADT, is the ultimate GUI to set up, launch and analyze 
AutoDockruns. With ADT, you can:

    View molecules in 3D, rotate & scale in real time.
    Add all hydrogens or just non-polar hydrogens.
    Assign partial atomic charges to the ligand and the macromolecule 
      (Gasteiger or Kollman United Atom charges).
    Merge non-polar hydrogens and their charges with their parent carbon 
    Set up rotatable bonds in the ligand using a graphical version of 
    Set up the AutoGrid Parameter File (GPF) using a visual representation 
      of the grid box, and slider-based widgets.
    Set up the AutoDock Parameter File (DPF) using forms.
    Launch AutoGrid and AutoDock.
    Read in the results of an AutoDock job and graphically display them.
    View isocontoured AutoGrid affinity maps.

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