What if I have a question that is not answered here or in the manual? Installation Questions. How is dms installed? Should AMBERHOME be. This tutorial introduces DOCK Score in DOCK6 and describes the preparation of input Please see the DOCK6 manual for futher details. If you have installed DOCK6, this script can be found in the bin directory. . To select other options, please read the DOCK 6 Manual.

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It should also be noted that the computational experiments described here all employ a rigid receptor.

DOCK tutorial with Streptavidin – Rizzo_Lab

This will not cause any trouble in most of the time, but you may doc,6 to notice this in some circumstances, for example when you want to execute some. The RGD protocol shows an approximately linear increase in docking run time as ligand flexibility increases, as expected, and the average docking run time for ligands of 17 or fewer rotatable bonds is three minutes or less.

The difference is that the reference molecule for the upper case is the original ligand. Cross-docking outcomes for 24 families. File paths that need to be specified are listed below:. Docking Forensic Tools Careful analysis of the docking process and outcomes, particularly the docking failures, is a means of discovering problems in or limitations of the DOCK codebase, input parameters, or structure preparation protocols.

Cross-docking to the neuraminidase family results in 0.

DOCK 6: Impact of New Features and Current Docking Performance

This observation follows our expectations, and it demonstrates that DOCK performs optimally when searching for cognate receptor-ligand binding poses.

Overall, these works represent as yet unreported novel docking results, obtained with newly added DOCK functionality, over a significantly large validation test set systems.


And then use the ViewDock function of Chimera to look at your 47 ligands one or however many you want at a time. Overlay of ligands from the cyclooxygenase family. This program can either be used interactively, or an input file can be fed in, just like the showbox program. For those succesfully docked ligands, the file will return the elapsed time for docking, and for those not succesfully docked, it will return an error massege like this:.

Parallel computing can reduce the running time of virtual screening.

2012 DOCK tutorial with Streptavidin

After performing virtual screening on Seawulf or any other computer, if you are using a parallel computer, you should manuao a multi-mol2 file 1DF8. Parameters requiring specification are listed below:. Since the computational cost of virtual screening is much higher than single-ligand docking, it is better for us to run it on Seawulf.

Unable to save thumbnail to destination. In preparation for cross-docking, we found that the three lapatinib-like ligands were incompatible with 11 of the 12 active forms of the receptor Figure 14also see Supporting Information Figure S For simplicity we keep most of the answers as default.

The streptavidin monomer is composed of eight antiparallel beta-strands which folds to give a beta barrel tertiary structure. It is a co-enzyme that is required in the metabolism of fatty acids and leucine. A high clash overlap parameter near 1 can negatively impact sampling, while a low parameter near 0 can allow too manuao unphysical ligand conformers to appear. Importantly, the alternative poses determined by the 1-anchor or 3-anchor protocols always yielded less favorable energy scores than the poses found using the standard protocol, manuao the improved sampling attained by using more anchors per molecule.

The first set of key experiments, pose reproduction calculations, were performed using the standard FLX protocol with the SGE scoring function over the SB test set and three different versions of DOCK including the current version 6. Molecules shown were selected based on the top 5 scored results obtained with the standard protocol. Morton A, Matthews BW. Hydrogen atoms hidden for clarity. It is important to emphasize that the correlation of low success rates with faster run times often indicates undersampling caused by early termination of docking calculations.


In practice, we find essentially no difference in docking darunavir to any form of protease. The one with the best grid score With the internal energy function, more branches contain physically acceptable conformations, resulting in improved sampling.

DOCK 6: Impact of New Features and Current Docking Performance

In this case, you majual find them before you delete one sphere and you dick6 to repeat this one more time to delete another one. The purpose of this manuscript is to introduce and discuss several important updates to the DOCK 6 codebase, focused on version 6. Briefly, for every non-bonded pair of ligand atoms, the clash overlap function sums the two van der Waals radii and multiplies that value by a user-specified clash overlap parameter ranging from 0 to 1.

With the current protocols, it is important to elaborate that docking may only be able to discriminate between strong and weak binders in cases where mutations directly interact with the ligand; docking should not be expected to be sensitive to mutations with indirect effects, including solvation or allosteric changes, for example. A major update to the DOCK descriptor scoring function has been made that allows different functions to be combined in the form:

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