http://haddock.science.uu.nl News feed of the HADDOCK software webportal Fri, 12 Mar 2010 09:47:00 GMT Thu, 11 Mar 2010 09:47:00 GMT Weblog Editor 2.0 en-us Wed, 10 Feb 2010 23:11 GMT Alexandre Bonvin http://haddock.science.uu.nl/services/HADDOCK/haddock.php
We are glad to announce a major upgrade in the HADDOCK server.

The HADDOCK server now includes a multi-body docking interface, supporting the docking of up to six partners, in any combination of protein, DNA, peptide and small molecules. Like in two-body docking, each partner can contain one or more chains, and ensemble PDBs are supported.

In addition, we have developed the prediction interface, which is a docking protocol optimized for docking driven by bioinformatic interface predictions (with high sensitivity) instead of experimental data. Here by default 87.5% of the data will be discarded at random for each docking trial.

Finally, there is the refinement interface, which allows HADDOCK refinement and scoring of protein complexes or rigid-body docking solutions.

The default parameter setting for the various interfaces is listed on the HADDOCK web server page.

The HADDOCK server has been running until now on a 2.1beta version of HADDOCK, which has just been finalized and will soon be released to the public.

The prediction interface is open to all registered HADDOCK server users. The multibody and refinement interfaces require guru level access, which can be granted upon request.

We have seen a load increase over the last couples of months and as a result the waiting time has also increased. You might consider making use of the Grid-enabled HADDOCK server available via www.enmr.eu/webportal. This version however requires a valid Grid certificate. Instructions for registration can be found at www.enmr.eu/registration



When using the HADDOCK server in your work, please cite our upcoming Nature Protocols paper in your publications:

S.J. de Vries, M. van Dijk and A.M.J.J. Bonvin. The HADDOCK web server for data-driven biomolecular docking. Nature Protocols, in press.

Best regards,

The HADDOCK server team]]> 10 Mar 2009 16:33 GMT Alexandre Bonvin http://gridtalk-project.blogspot.com/2009/03/e-nmr-for-grid-powered-protein.html
Held from March 2-6, the event was a showcase for grid technologies and connected developers, users and newcomers to distributed computing. The e-NMR team was present to introduce the benefits of the e-nmr grid platform for structural biology, a user-friendly interface that allows scientists to easily access grid computing resources to power simulations of protein structure.

The live demonstration of 'grid-powered protein structure simulations' by the e-NMR team was awarded 'Best application demo' by the organization comity. The award signified a unique and important application that was adopted to the grid very fast, had a clear development strategy and brought new resources to the grid. You can watch a sort movie of the demonstration here]]> 05 Jan 2010 13:23 GMT Marc van Dijk http://haddock.science.uu.nl/dna/benchmark.html Benchmark version 1.2: Small fixes in residue mapping for two entries. For two entries (1EYU,1RVA) to unbound protein was composed out off two distinct subunits. These have now been separated into individual pdb files and all other files have been adjusted accordingly. Version 1.2 can be downloaded from the benchmark page as a gzipped file. 02 Sep 2008 11:50 GMT Alexandre Bonvin http://haddock.science.uu.nl/services/HADDOCK/haddock.php
Today we welcome HADDOCK user number 500.
We would like to thank all HADDOCK users for the many positive responses and feedback that help use further improve and develop the software.

Always onto the next milestone,
The HADDOCK team]]> 14 Aug 2008 21:22 GMT Marc van Dijk http://haddock.science.uu.nl/dna/benchmark.html Version 1.1 of the protein-DNA docking benchmark has been released. The update contains some minor improvements and bug fixes. The bound to unbound residue mapping file (profit.dat) has been redesigned to make it more flexible in use. The PDB structure file that represents the complex reconstructed from the unbound processed components after superimposition contained more than one instance of the same complex coordinate set. This has been fixed. Version 1.1 can be downloaded from the benchmark page as a gzipped file. 25 Jun 2008 17:17 GMT Alexandre Bonvin http://haddock.science.uu.nl/services/HADDOCK/haddock.php http://www.haddock.science.uu.nl/alink.jpg http://www.nmr.chem.uu.nl
It is my pleasure to announce our new HADDOCKing web server accessible from the following addresses:

http://haddock.science.uu.nl
http://www.haddocking.org
http://www.haddocking.eu

The server allows easy access to information-driven docking with HADDOCK and is freely accessible for non-profit users upon registration.

The server runs version 2.1 of HADDOCK which has several small improvements to make it more robust for all kinds of errors and problems (we will distribute this version later this year). The server has four access levels accessible from the main server page

easy interface This interface allows you to define the structure for each molecule you want to dock as well as the residues belonging to the interaction interface. Docking is performed with default settings that work well for average complexes. If you do not have any special wishes for the system you want to have docked, this is the way to go.

expert interface This interface provides more control over HADDOCK parameters and supports additional types of restraints. It also allows you to upload your own ambig and unambig restraint files as well as hydrogen bond and dihedral angle restraints

guru interface This interface provides full control over HADDOCK parameters and supports a wide range of experimental restraints including residual dipolar couplings and diffusion anisotropy

file upload interface This interface allows you to upload HADDOCK parameter files that have been generated previously by the server upon submission. Note that in the future, CCPN Analysis will support direct generation of such parameter files.

Access is initially granted to the easy interface, but experienced HADDOCK users can request access to other interfaces.

The server supports both protein and RNA/DNA. For the latter, the input structures are processed to automatically generate dna-rna restraint files. Further, the server can automatically (default setting) determine the protonation state of histines by calling the Whatif server and also contact the PRODRG server in case of missing parameters for co-factors or ligands. Default settings of the server can be found here

The results are presented on a web page providing cluster statistics. The top four models of each cluster are available for download or can be visualized directly with Jmol. A complete gzipped tar file of the run directory can be downloaded as well. An output example can be found here

We are now working within the European eNMR project toward making the HADDOCK server gridable which should increase our computational capacity in the future.

We hope that this resource will be useful to the community and welcome any feedback.

Finally, I want to especially thank Sjoerd de Vries and Marc van Dijk from my group for developing this web resource.

Cheers,
Alexandre]]>