Corporate Banner
Satellite Banner
Proteomics
Scientific Community
 
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
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 2,500+ scientific posters on ePosters
  • More than 3,700+ 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.


Scientific News
Liquid Biopsies: Utilization of Circulating Biomarkers for Minimally Invasive Diagnostics Development
Market Trends in Biofluid-based Liquid Biopsies: Deploying Circulating Biomarkers in the Clinic. Enal Razvi, Ph.D., Managing Director, Select Biosciences, Inc.
Self-Assembling, Biomimetic Membranes May Aid Water Filtration
A synthetic membrane that self assembles and is easily produced may lead to better gas separation, water purification, drug delivery and DNA recognition, according to an international team of researchers.
Crystal Clear Images Uncover Secrets of Hormone Receptors
NIH researchers gain better understanding of how neuropeptide hormones trigger chemical reactions in cells.
Error Correction Mechanism in Cell Division
Cell biologists have reported an advance in understanding the workings of an error correction mechanism that helps cells detect and correct mistakes in cell division early enough to prevent chromosome mis-segregation and aneuploidy, that is, having too many or too few chromosomes.
Crucial for Stem Cell Survival Protein Identified Using Editing Tool CRISPR
A team of University of Wisconsin-Madison engineers has identified a protein that is integral to the survival and self-renewal processes of human pluripotent stem cells (hPSC).
Sorting Through Cellular Statistics
Aaron Dinner, professor in chemistry, and his graduate student Herman Gudjonson are trying to read the manual of life, DNA, as part of the Dinner group’s research into bioinformatics—the application of statistics to biological research.
First Artificial Ribosome Designed
Researchers at the University of Illinois at Chicago and Northwestern University have engineered a tethered ribosome that works nearly as well as the authentic cellular component, or organelle, that produces all the proteins and enzymes within the cell.
The Genetic Roots of Adolescent Scoliosis
Scientists at the RIKEN Center for Integrative Medical Sciences in collaboration with Keio University in Japan have discovered a gene that is linked to susceptibility of Scoliosis.
HIV Susceptibility Linked to Little-Understood Immune Cell Class
High levels of diversity among immune cells called natural killer cells may strongly predispose people to infection by HIV, and may be driven by prior viral exposures, according to a new study.
New Tech Enables Epigenomic Analysis with a Mere 100 Cells
A new technology that will dramatically enhance investigations of epigenomes, the machinery that turns on and off genes and a very prominent field of study in diseases such as stem cell differentiation, inflammation and cancer has been developed by researchers at Virginia Tech.
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
2,500+ scientific and medical posters
A library of 2,500+ scientific videos on LabTube
3,700+ scientific videos
Close
Premium CrownJOIN TECHNOLOGY NETWORKS PREMIUM FREE!