What are the XedTools?

The XedTools provide you with access to one of the most innovative molecular mechanics force fields currently in existence. XED uses off atom charges on electronegative atoms to give a more accurate representation of the charge density surrounding an atom, resulting in an improved description of molecular interactions. The XedTools currently encompass conformer generation and ligand minimization:

XedeX conformation generation

XedeX is a force field conformation explorer that uses our unique XED force field. XedeX is optimized to produce a diversity of energy minimized ligand conformations in a small number of conformations. XedeX performance is exceptional, reproducing the ligand bioactive conformation in 100 conformations in the majority of drug-like ligands. Using XedeX gives you:

• Diverse conformation populations
• Energetically accessible and realistic conformation populations
• Excellent control over your conformation generation experiments
• Conformations that are fully minimized in the XED force field

XedeX is available as a command line binary that can be incorporated into Workflow applications or used standalone. It is an integral part of torchV10, forgeV10, blazeV10 and sparkV10 database generator.

XedMin ligand minimization

The XED force field lies at the heart of Cresset’s unique technology. The use of off-atom charges enables an improved description of intermolecular interactions and molecular fields. XedMin enables ligand minimization with the XED force field. Using XedMin gives you:

• Accurate, experimentally validated intermolecular interactions.
• Correct minimization of pi-pi interactions.
• Correct prediction of cation-pi interactions.
• Anisotropic charges and polarizability.
• Improved molecular electrostatics.

XedMin is available as a command line binary that can be incorporated into Workflow applications or used standalone. It is an integral part of all Cresset’s products and is available as a free download.

Access the advanced, radical features of the XED force field

The XED force field reliably reproduces experimentally observed intramolecular interactions and bioactive conformations. A systematic study on a large dataset showed that XedeX performs exceptionally well at reproducing bioactive conformations.

XedeX conformations of ligand from pdb code 1g9v showing the conformation closest to the bioactive conformation in CPK with green carbons.

Interfaces

The XedTools are available as command line binaries that can be scripted or accessed from workflow protocols and nodes. Command line binaries give you the ultimate flexibility to deploy Cresset’s unique science in the way that you want it. Simple, standardized switches enable you to tailor the calculation to exactly meet the demands of your experiment. Detailed documentation, either as PDF files for printing or Linux ‘man’ pages provide both background knowledge and foreground understanding to rapidly create your perfect command. Pipeline Pilot protocols for all the XedTools are available for free. The protocols can be used immediately within Discovery Studio or customized for deployment in larger workflows. KNIME nodes for all the XedTools are available for free. The nodes can be easily combined into greater workflows, either with other Cresset applications or with nodes from 3rd parties.