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AutoDock4.2.6 [1%] by rhuey, 2014-08-04 11:53
AutoDock4.2.6 features improved input checking and an output format suitable for automated analysis.
How-to dock a ligand with many torsions [1%] by rhuey, 2013-01-15 13:44
Two types of special treatment for systems with many torsions are described which may enable the user to get reproducible results when docking molecules with ...
AutoDock4.2.5.1 [1%] by rhuey, 2013-01-03 13:46
New AutoDock version fixes bug in version 4.2.5
Adding new atom parameters to AutoDock [1%] by rhuey, 2011-07-06 10:00
To use AutoDock with molecules that have atoms of types not included in the AutoDock force field calibration such as heavy metal ions, estimate values of Rii, ...
Why do the results differ when multiple dockings are done with the same input? [1%] by rhuey, 2009-07-06 11:18
Multiple docking calculations are specified in a docking parameter file using one of the following keywords: 'ga_run', 'do_local_only' or 'runs' plus ...
Force a non-rotatable bond to be considered rotatable in ADT [1%] by rhuey, 2008-10-28 16:47
ADT discriminates between rotatable bonds and non-rotatable bonds during ligand preparation. If bonds are classified as rotatable when they should be ...
Using AutoDock 4 for Virtual Screening [1%] by rhuey, 2008-01-29 06:49
This teaches you not only how to use AutoDock 4 to perform virtual screening using AutoDock 4, but also a lot about using UNIX to organize and process large ...
How can I determine if a bond is rotatable in a ligand pdbq(t) file [1%] by rhuey, 2007-08-01 11:31
The flexibility pattern for a ligand is encoded in its written pdbq(t) file by the inclusion of specific AutoDock keywords ROOT/ENDROOT, BRANCH/ENDBRANCH. ...
Which library should I use for virtual screening? [1%] by rhuey, 2007-07-19 17:57
There are a variety of libraries that can be used for screening, which one should I use?
How to prepare a text summary of a directory of AutoDock4 docking results [1%] by rhuey, 2007-12-07 19:23
This How-to explains how to use the python script "summarize_results4.py" to create a text file which summarizes the results of all the AutoDock4 log files in ...
How to prepare a flexible residue file for AutoDock4 [1%] by rhuey, 2007-08-27 14:22
This How-to explains how to use the python script "prepare_flexreceptor4.py" to create two input receptor files for AutoDock4, one containing the rigid ...
How to prepare a docking parameter file for AutoDock4 [1%] by rhuey, 2007-08-27 14:21
This How-to addresses using the python script 'prepare_dpf4.py' to create a docking parameter file for AutoDock4. This docking parameter file specifies the ...
How to prepare a grid parameter file for AutoGrid 4 [1%] by rhuey, 2010-05-18 13:40
This How-to addresses using the python script 'prepare_gpf4.py' to create a grid parameter file for AutoGrid4. This grid parameter file specifies the 3D ...
How to prepare a receptor file for AutoDock4 [1%] by rhuey, 2010-11-19 14:08
This How-to addresses using the python script 'prepare_receptor4.py' to format a receptor file for AutoDock4. Input files for this script can be in pdb, pdbq, ...
How to prepare a ligand file for AutoDock 4 [1%] by rhuey, 2007-08-27 14:17
This How-to explains how to use the Python script 'prepare_ligand4.py' to format a ligand file for AutoDock 4. Input files for this script can be in PDB, ...
rhuey [1%] by rhuey, 2006-08-29 08:16

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