" "
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 2,900+ scientific posters on ePosters
  • More Than 4,200+ 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 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
Breaking Cell Barriers with Retractable Protein Nanoneedles
Adapting a bacterial structure, institute researchers have developed protein actuators that can mechanically puncture cells.
Gene Signature could Lead to a New Way of Diagnosing Lyme Disease
Lyme disease patients had distinctive gene signatures that persisted for at least three weeks, even after they had taken the antibiotics.
Retractable Protein Nanoneedles
The ability to control the transfer of molecules through cellular membranes is an important function in synthetic biology; a new study from researchers at Harvard’s Wyss Institute for Biologically Inspired Engineering and Harvard Medical School (HMS) introduces a novel mechanical method for controlling release of molecules inside cells.
Leukemia’s Surroundings Key to its Growth
Researchers at The University of Texas at Austin have discovered that a type of cancer found primarily in children can grow only when signaled to do so by other nearby cells that are noncancerous.
Common Cell Transformed into Master Heart Cell
By genetically reprogramming the most common type of cell in mammalian connective tissue, researchers at the University of Wisconsin—Madison have generated master heart cells — primitive progenitors that form the developing heart.
‘Smelling’ Prostate Cancer
A research team from the University of Liverpool and the University of the West of England (UWE Bristol) has reached an important milestone towards creating a urine diagnostic test for prostate cancer that could mean that invasive diagnostic procedures that men currently undergo eventually become a thing of the past.
Genetic Mutation that Prevents Diabetes Complications
The most significant complications of diabetes include diabetic retinal disease, or retinopathy, and diabetic kidney disease, or nephropathy. Both involve damaged capillaries.
A Crystal Clear View of Biomolecules
Fundamental discovery triggers paradigm shift in crystallography.
Could the Food we Eat Affect Our Genes?
Almost all of our genes may be influenced by the food we eat, according to new research.
NIH Seeks Research Applications to Study Zika in Pregnancy, Developing Fetus
Institute has announced that the new effort seeks to understand virus effect on reproduction and child development.
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
2,900+ scientific and medical posters
A library of 2,500+ scientific videos on LabTube
4,200+ scientific videos
Close
Premium CrownJOIN TECHNOLOGY NETWORKS PREMIUM FOR FREE!