Corporate Banner
Satellite Banner
Technology
Networks
Scientific Communities
 
Become a Member | Sign in
Home>News>This Article
  News
Return

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 www.cresset-group.com/cgi-bin/demo.cgi.

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 www.cresset-group.com/cgi-bin/torchlite.cgi.

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 5,000+ 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 TechnologyNetworks.com 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.

Related Content

Cresset and Redx Pharma Announce Major Drug Discovery Collaboration
Cresset will provide consulting services in the area of candidate selection across a broad range of therapeutic areas and targets.
Wednesday, August 24, 2011
Scientific News
Point of Care Diagnostics - A Cautious Revolution
Advances in molecular biology, coupled with the miniaturization and improved sensitivity of assays and devices in general, have enabled a new wave of point-of-care (POC) or “bedside” diagnostics.
Mass Spec Technology Drives Innovation Across the Biopharma Workflow
With greater resolving power, analytical speed, and accuracy, new mass spectrometry technology and techniques are infiltrating the biopharmaceuticals workflow.
One Step Closer to Precision Medicine for Chronic Lung Disease Sufferers
A study led by University of North Carolina at Chapel Hill, and National Jewish Health, has provided evidence of links between SNPs and known COPD blood protein biomarkers.
Charles River Acquires Agilux
Enhances Charles River’s early-stage capabilities in bioanalytical services.
Scientists Find Lethal Vulnerability in Treatment-Resistant Lung Cancer
The study describes how the drug Selinexor killed lung cancer cells and shrank tumors in mice when used against cancers driven by the aggressive and difficult-to-treat KRAS cancer gene.
How Baby’s Genes Influence Birth Weight And Later Life Disease
The large-scale study could help to target new ways of preventing and treating these diseases.
Genes Underlying Dogs’ Social Ability Revealed
The social ability of dogs is affected by genes that also seem to influence human behaviour, according to a new study from Linköping University in Sweden.
Drug to Treat Alcohol Use Disorder Shows Promise Among Drinkers With High Stress
The findings suggest that potential future studies with drugs targeting vasopressin blockade should focus on populations of people with AUD who also report high levels of stress.
C Dots Show Powerful Tumor Killing Effect
Nanoparticles known as Cornell dots, or C dots, have shown great promise as a therapeutic tool in the detection and treatment of cancer.
Faecal Bacteria Linked to Body Fat
Researchers at King’s College London have found a new link between the diversity of bacteria in human poo – known as the human faecal microbiome - and levels of abdominal body fat.
Scroll Up
Scroll Down
Skyscraper Banner

Skyscraper Banner
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
5,000+ scientific videos
Close
Premium CrownJOIN TECHNOLOGY NETWORKS PREMIUM FOR FREE!