The new version of our popular XedTools is now available. XedTools 3.0 includes new functionality and the latest version of our XED force field.
The new force field incorporates:
- a completely analogue system for dealing with nitrogen atoms, enabling smooth transition from pyramidal to planar geometries
- enhanced description of aromatic halogen interactions
- support for some boronates and silicates.
The XedTools package consists of:
XedMin is Cresset’s free ligand minimizer used by thousands of our customers. This version includes important new functionality. A new command line switch enables the loading of a protein molecule so that ligands can be minimized within a protein context. Minimizing a set of docking poses in the XED force field can now be achieved using a simple script. Note that in this release the protein is limited to less than 15,000 total atoms (around 500 residues), is held completely static during the minimization and is not output at any stage. Register for a free XedMin license here.
XedeX is an integral part of all of Cresset’s applications; it is used to explore the conformations of molecules before adding them to databases or comparing molecules using fields. It is force field based so that all conformations are realistic, energy minimized structures. In our studies it performs excellently in reproducing bioactive conformations for molecules with less than 8 rotatable bonds. This version includes numerous tweaks to improve performance and an expanded ring library to include quinoline- and isoquinoline-containing structures.
XedConvert has been an integral part of our virtual screening system Blaze for some time but is a new addition to the XedTools package. Unsurprisingly, XedConvert is used to convert molecules between file formats and between 2D and 3D. It reads molecules in smiles, sdf, sdf3000, mol2, pdb and our own xed format and writes molecules in sdf, mol2 and xed formats. Given 1D or 2D data it will convert to 2D and 3D respectively, adding Cresset’s molecular fields as required. If you are planning on using XedMin to minimise ligands in the active sites of a protein then we recommend that you convert the protein in xed format first using XedConvert. As with all our command line tools, XedConvert can be combined with other applications in a pipe as it uses STDIN and STDOUT by default.
A free 12 month license to XedConvert is included with every request for a XedMin license, just register for a free XedMin license here.
We are currently working to integrate the new features in this release of XedTools into our KNIME nodes. The current XedeX and XedMin binaries should work seemlessly with the existing release and we expect to have new nodes available shortly.
To register for a free demo of XedeX or take a free 12 month license to XedMin or XedConvert simply register here and we’ll send you a license file.