News

XedTools 3.1 released

Version 3.1 of our popular XedTools package is now available. The XedTools package provides access to our unique molecular mechanics force field in the form of:

  • XedeX for conformation exploration
  • XedMin for ligand minimization
  • XedConvert for addition of our field points to molecules.

All binaries receive minor updates in this release and we have generated new recommended settings for XedeX (below). However, the new addition in this release is the incorporation of visualization plugins that enable the viewing of Cresset’s field points in third party applications.

Visualization plugins

The new plugins for PyMol and MOE enable the loading and display of a molecule that includes Cresset’s field points. This is achieved using XedConvert to generate the field points then display of the points in the third party application. The plugins are easy to load and bring in new command line and menu entries that enable the display of field points from sdf files.

Cresset Field Points in PyMol

XedeX

This release of XedeX brings new recommended settings for conformation hunting and new options that enables the specified bonds to be held rigid during conformation hunting. This last addition is particularly in situations where you are exploring a library design and want to keep specific parts of the molecules stationary but fully explore the conformations of variable sections of the scaffold. This is a vital addition to workflow scenarios and hence it will be part of our KNIME and Pipeline Pilot components in their release next month.

The performance of XedeX was assessed in an independent study in 2013 where the conclusion was that it performed as well or better than all other conformation hunting applications. In this release we have included some minor enhancements that we are confident will improve the performance further. However, we have also taken another look at the options that we use in XedeX in different situations with the result that we have new recommendations for generating the best possible population of conformations. The table below outlines the new results.

Conditions Relative time Average RMSD Average confs Command line switches
Current best 1 0.66 152 -a t -D 5 -A -T 90 -m 200 -f 0.5 -r 0.5 -E 6
New best 5 0.66 124 -a t -D 5 -A -T 90 -m 200 -f 0.5 -r 0.1 -E 3
Current diverse 0.5 0.74 65 -a t -D 5 -A -T 90 -m 200 -f 1.0 -r 0.5 -E 6
New diverse 2.5 0.74 55 -a t -D 5 -A -T 90 -m 200 -f 1.0 -r 0.1 -E 3

The experiment: For all pdb ligands in set (190), create conformation populations starting with 2D structure then measure lowest RMSD between bioactive conformation and conformation population. Record time taken for complete set, average number of conformations and average RMSD.

XedeX conclusion

This new version of XedeX can reduce the energy window of the conformations that are kept which resulted in fewer and better conformations in the population with a greater probability of reproducing the bioactive conformation. These results are true no matter what other options are chosen, but in all cases the time taken to produce the population increased. Our recommendation is to keep the existing settings for normal use but to use new options when accuracy is more important than time. As a result our ‘Accurate’ methods in Torch and Forge have been updated with the new options and we recommend them to all our command line users.

Try XedTools

Our registration page will give you a 12 month license to XedMin and the Visualization Plugins as well as a 1 month evaluation license to XedeX. To upgrade your current installation contact Cresset support for a download link. To add the Visualization Plugins to your current installation just download this zip file.

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