Corporate Banner
Satellite Banner
Scientific Community
Become a Member | Sign in
Home>News>This Article

XedTools 3.0 Released

Published: Monday, March 18, 2013
Last Updated: Monday, March 18, 2013
Bookmark and Share
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.

Further Information

Join For Free

Access to this exclusive content is for Technology Networks Premium members only.

Join Technology Networks Premium for free access to:

  • Exclusive articles
  • Presentations from international conferences
  • Over 3,500+ scientific posters on ePosters
  • More than 5,200+ scientific videos on LabTube
  • 35 community eNewsletters

Sign In

Forgotten your details? Click Here
If you are not a member you can join here

*Please note: By logging into you agree to accept the use of cookies. To find out more about the cookies we use and how to delete them, see our privacy policy.

Scientific News
Integrated Omics Analysis
Studying multi-omics promises to give a more holistic picture of the organism and its place in its ecosystem, however despite the complexities involved those within the field are optimistic.
RNA-Binding Proteins Role in ALS Revealed
Researchers describe how damage to RNA-binding protein contributes to ALS, isolating a possible therapeutic target.
Advances in Alzheimer’s Research
Researchers show how a diseased vertebrate brain can naturally react to Alzheimer’s pathology by forming more neurons.
NIH Study Determines Key Differences between Allergic and Non-Allergic Dust Mite Proteins
Researchers at NIH have uncovered factors that lead to the development of dust mite allergy and assist in the design of better allergy therapies.
Study Finds Key Regulator in Pulmonary Fibrosis
Researchers identify an enzyme that could open the way to therpies for chronic fatal lung disease.
Alzheimer’s-Linked Protein May Play Role in Schizophrenia
Researchers suggests a protein linked to cognitive decline in Alzheimer's also plays a role in genetic predisposition to schizophrenia.
Peptides vs. Superbugs
Scientists successfully develop a shuttle system made of liquid-crystalline nanomaterials that protect peptites.
Cocoa Compound Linked to Some Cardiovascular Biomarker Improvements
The study highlights the urgent need for large, long-term RCTs that improve understanding of how the short-term benefits of cocoa flavanol intake on cardiometabolic biomarkers may be translated into clinical outcomes.
Immune Approach Targets Humans Instead of Bacteria
Scientists show for the first time how bacterial superantigen toxins work, and how short peptides can block them and save lives.
Could 2D Mass Spec Breakthrough Lead to Medical Revolution?
Pharmaceutical research could be quicker and more precise, thanks to an innovative breakthrough in 2D mass spec from the University of Warwick.
Scroll Up
Scroll Down
Skyscraper Banner

SELECTBIO Market Reports
Go to LabTube
Go to eposters
Access to the latest scientific news
Exclusive articles
Upload and share your posters on ePosters
Latest presentations and webinars
View a library of 1,800+ scientific and medical posters
3,500+ scientific and medical posters
A library of 2,500+ scientific videos on LabTube
5,200+ scientific videos