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XedTools 3.0 Released

Published: Monday, March 18, 2013
Last Updated: Monday, March 18, 2013
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Next generation of XED force field enables accurate modelling of ligand-protein interactions.

Cresset has announced a new release of the popular XedTools package, including the next generation of the popular XED force field.

The XedTools package contains command line utilities for studying molecular interactions using the XED molecular mechanics force field.

This release brings an update to the free XedMin tool so that ligands can now be minimized within a protein context, giving significantly more accurate modelling of protein ligand interactions.

The new XED force field incorporates
• enhanced description of aromatic-halogen interactions, an area of active interest to chemists designing novel medicines
• a completely analogue system for dealing with nitrogen atoms, enabling a smooth transition from pyramidal to planar geometries
• an extension of the supported elements to enable the modeling of compounds with new mechanisms of action such as boronates.

Further new capabilities in the XedTools package are outlined below.

Easily minimize ligands within a protein active site using XedMin
XedMin, Cresset’s free ligand minimization engine, has been extended to enable the loading of a protein molecule so that ligands can be optimized within a protein context.

XedMin can now rapidly minimize of a set of ligands within the active site of a protein.

The ligands could be poses from a docking engine or ligand alignments from Cresset’s suite of ligand similarity applications. Using the XED force field ensures that important interactions such as aromatic-aromatic stacking, cation-pi interactions, or the increasingly interesting halogen-aromatic stacking can now be modelled rapidly and accurately. XedMin is available free from

Improved performance of the XedeX conformation hunter
XedeX is used to explore the conformations of molecules and is an integral part of all of Cresset's software. Because it is force-field based, all of the conformations are realistic, energy minimized structures.

In studies it performs particularly well at reproducing bioactive conformations for molecules with less than eight rotatable bonds. This version offers improved performance, enhanced capabilities and an expanded ring library to improve the conformations of molecules with flexible rings.

Of particular note is the new ability to conformationally explore only selected portions of a molecule, keeping the remainder in a fixed orientation. This capability enables the exploration of flexible side chains on proteins or peptides with defined secondary structures as well as small molecules where the core takes up a specific or constrained shape.

Create 3D representations with XedConvert
XedConvert, an integral part of Cresset’s virtual screening system blazeV10, is newly released as part of the XedTools package. A free 12 month license to XedConvert is available free from

XedConvert is used to convert molecules between file formats and between 2D and 3D. It reads molecules in smiles, sdf, sdf3000, mol2, pdb and Cresset’s 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.

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