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AD4.1_extended.dat [1%] by morris, 2009-05-29 09:43
This is the default parameter file for AutoGrid 4.0.0 and AutoDock 4.0.1. It can also be used as an alternative parameter file for AutoGrid 4.2 and AutoDock ...
AD4.1_compact.dat [1%] by morris, 2009-05-29 08:56
The coefficients of this model were derived using the assumption that the unbound ligand is in the compact conformation. This is not currently supported in ...
AD4.1_bound.dat [1%] by morris, 2009-05-29 09:42
This is the default parameter file for AutoGrid 4.2 and AutoDock 4.2; the coefficients of this model were derived using the assumption that the unbound ligand ...
AD4_parameters.dat [1%] by morris, 2008-03-12 13:11
This is the default parameter file for AutoGrid 4.0.0 and AutoDock 4.0.1; the coefficients of the model were derived using the assumption that the unbound ...
makebox [1%] by morris, 2008-02-08 13:36
This script is used with a GPF to create a PDB file that shows the extent of the AutoGrid box. Suggested usage is: makebox <molecule.gpf> > ...
Scripts [1%] by morris, 2008-02-08 13:36
This provides a range of scripts useful when using AutoDock. They should run on Cygwin, Linux, Mac OS X and other Unix platforms. They are written in csh, ...
Instructions: Using AutoDock 4 for Virtual Screening (PDF document, 464 KB) [1%] by morris, 2008-01-29 04:19
Step-by-step instructions explaining how to set up, run and analyse a virtual screening experiment using AutoDock 4.
Presentation: Using AutoDock 4 for Virtual Screening (Handouts, PDF document, 1.1 MB) [1%] by morris, 2008-01-27 19:27
These are the slides introducing the virtual screening tutorial for AutoDock version 4.
How should I prepare a ligand for docking with AutoDock? [1%] by morris, 2007-12-18 23:05
Where can I obtain 3D coordinates for my ligand? What do I have to do before I can use AutoDock?
autodock3: wrong number of values read in. Check grid map! [1%] by morris, 2007-12-18 20:20
When using AutoDock, I get the error message: "autodock3: wrong number of values read in. Check grid map!".
Where can I find the Python scripts for preparing and analysing AutoDock dockings? [1%] by morris, 2008-01-30 09:58
I've read about the Python prepare scripts like "prepare_dpf4.py" in places like the virtual screening tutorial. This FAQ answers the questions, "Which Python ...
AutoDock's role in Developing the First Clinically-Approved HIV Integrase Inhibitor [1%] by morris, 2007-12-17 18:18
Prof. J. Andrew McCammon and his colleagues used AutoDock and the Relaxed Complex Method to discover discover novel modes of inhibition of HIV integrase. ...
ADT: "formatted for autodock4, unable to save in autodock3 format" [1%] by morris, 2007-12-07 17:49
I am unable to save the ligand PDBQ file in AutoDock 3 format in AutoDockTools/ADT. The message that comes up says "formatted for autodock4, unable to save in ...
How do I do a local energy minimisation? [1%] by morris, 2007-12-07 17:10
If I specify "do_local_only" in the DPF, what exactly is being energy-minimised?
How do I add new atom types to AutoDock 4? [1%] by morris, 2007-07-26 18:31
AutoDock version 4.0 has parameters for H, C, N, O, F, Mg, P, S, Cl, Ca, Mn, Fe, Zn, Br and I. What do you do if your molecule has an atom type that isn't ...
In a flexible receptor docking in AutoDock 4, which atoms are used in the clustering? [1%] by morris, 2007-07-24 16:44
When AutoDock 4 performs conformational clustering on the docking results, which atoms are used in the clustering?
What should I look for when I visualize a docked compound? [1%] by morris, 2007-07-19 18:25
What features should I look for when I visualize a docked compound?
Will I need to visualize the virtual screening results? [1%] by morris, 2007-07-19 18:16
Will I need to visualize the virtual screening results?
What's the best way to analyze the results? [1%] by morris, 2007-07-19 18:13
After the virtual screening is finished, what's the best way to look at the results?
How do I know which docking results are "hits"? [1%] by morris, 2007-07-19 18:06
Which docking results should I consider as likely to bind well to my target?
How many dockings and energy evaluations should I use for each compound? [1%] by morris, 2008-03-06 20:58
How much computational time should be invested in each compound?
Is there a limit on the number of atoms in the ligand that can be used in AutoDock? [1%] by morris, 2007-06-26 16:57
Is there a limit on the size of the ligand molecule, and if so, how can I change it?
Formula for Determining the "Goodness of Hit Lists" in 3D Database Searches [1%] by morris, 2007-06-20 16:35
A measure of the 'Goodness' of hit lists obtained from chemical database searching is proposed (the G-H score). This measure takes into account both the yield ...
VI European Workshop on Drug Design - Molecular Docking Tutorial [1%] by morris, 2010-02-25 14:28
This is a tutorial given in the VI European Workshop in Drug Design, in Certosa di Pontignano (Siena, Italy) and was prepared by Rino Ragno (RCMD), Anna ...
Link to Tutorial [1%] by morris, 2013-06-17 12:01
You can find links to the AutoDock 4 tutorial from Rome Center for Molecular Design on this page.
How can I set up the protonation state of my histidine sidechains? [1%] by morris, 2007-05-25 17:25
Histidines can be neutral or positively charged. When neutral, they can be protonated at the delta (HD1) or epsilon (HE2) positions. How can I set these up?
Which values of the genetic algorithm parameters do you normally use? [1%] by morris, 2008-03-06 20:58
When running a docking using the GA (genetic algorithm) or LGA (Lamarckian GA), there are a number of parameters to set. Which values do you normally use?
Should I always use polar hydrogens? [1%] by morris, 2007-05-22 23:30
I know that AutoDock needs hydrogen atoms on the macromolecule and the ligand, but should I use polar hydrogens?
Where should I start ADT? [1%] by morris, 2007-05-22 23:18
If I want to start ADT from the UNIX/Linux/Mac OS X command line, where should I start it?
Is there a graphical user interface to AutoGrid and AutoDock? [1%] by morris, 2007-05-22 23:12
Is there a tool to help me set up my AutoGrid grid map calculations, and my AutoDock dockings? One that can help me analyse my docking results?

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