-
News & Events of 2009
e-NMR training workshop (November 4-6, 2009, Hinxton-Cambridge)
A workshop was organised in conjugation with CCPN and Extend-NMR at the EBI-EMBL in Hinxton-Cambridge, England.
Analysis of Security Issues (November, 2009, eNMR D3.9)
A document is available about the analysis of security issues brought about by the user community and by industrial stakeholders.
Survey (November, 2009, eNMR D2.8)
A document is available about the survey of the interest and demands of the user community as well as of potential industrial stakeholders with respect to the provision of fee-based services and/or training activities.
Annual Report on the Dissemination of e-NMR results (November, 2009, eNMR D1.7)
The report is available here.
Critical Assessment of Automated Structure Determination (CASD) of Proteins from NMR data
CASD-NMR is a rolling community-wide experiment involving developers of software tools / protocols for the automated calculation of protein structures from NMR data.
View the video presentation of the project presented at the EGEE 09 conference in Barcelona (September 2009)
New components' integration and deployment report (August 2009, eNMR D2.3)
A document is available about the integration into e-NMR grid of software components developed by the Joint Research Activities.
e-NMR training workshop (June 15-18, 2009, Florence, eNMR D1.5)
A workshop was organized in conjunction with the EAST-NMR project for bio-NMR users for training in using the e-NMR GRID. More details and a program can be found here.
e-NMR HADDOCK webportal tutorial released (May 2009, part of eNMR D3.5)
An online tutorial describing the use of the eNMR HADDOCK webportal with different kinds of NMR and bioinformatic prediction data is now available from the following link. In addition, a Flash movie describing the use of the HADDOCK portal can found here.
MDDnmr and MARS use cases released (May 2009, eNMR D3.1)
Use-cases are now available providing examples on how to run the MDDnmr and MARS software on the eNMR grid. See the WIKI for descriptions and downloads.
Practical courses "From NMR Data to Protein Structure" (from October 2009)
The course series, taught by Spronk NMR Consultancy, provides an introduction to protein NMR assignment and structure calculation using the latest CCPN software and CYANA. Course participants will be made familiar with the basic concepts of CcpNmr Analysis as well as typical protein NMR resonance assignment protocols using a real life example. The course will include an introduction and demonstration of structure calculations on the eNMR grid.
For more information and registration visit the course website "From NMR data to protein structure".
Overview of software for nucleic acids (eNMR D3.2)
A document describing the assessment of existing software, strategy and project planning is available here.
SOFTWARE Application workshop (May 2009, eNMR D1.2, D1.3)
Test files are available for the Software Application workshop. A document describing the files is available here. A report on the workshop and its results is available here (D1.3).
Biomed Grid School (May, 2009)
The INFN co-organised the Biomed Grid School in Varenna, Italy (10-15/5/2009)
Request for Enhancements of gLite to support bio-NMR applications (April 2009, eNMR D3.3)
The document describing this deliverable is available here.
Assessment of the e-NMR infrastructure and GOC report (April 2009, eNMR D2.2)
The document describing this deliverable is available here.
e-NMR CE-Rosetta web portal launched (April 1st 2009)
The CS-Rosetta portal can be accessed from access page of the eNMR web site.
-
News & Events of 2008
NUSSAMPLER use case released (December 2008, eNMR D3.1)
A use-case is now available providing examples on how to run non-linear sampling data processing on the eNMR grid with the program NUSSAMPLER. See the WIKI for description and download.
PROSA use case released (December 2008, eNMR D3.1)
A use-case is now available providing examples on how to run NMR data processing on the eNMR grid with the program PROSA. See the WIKI for description and download.
INFIT use case released (December 2008, eNMR D3.1)
A use-case is now available providing examples on how to run scalar coupling constant determination from inphase multiplets on the eNMR grid by the program INFIT. See the WIKI for description and download.
CYANA use cases released (November 2008, eNMR D3.1)
A number of use-cases are now available providing examples on how to run NOE assignment and structure calculations on the eNMR grid with CYANA. See the WIKI for description and download.The CYANA use cases include a basic structure calculation from given distance and torsion angle restraints, a structure calculation starting from manually assigned NOESY cross peaks, an example of combined automated NOE assignment and structure calculation, a structure calculation for a homodimeric protein, as well as structure calculations including residual diploar coupling constant restraints or pseudocontact shift restraints.
Training for Grid administarors and application developers (november/december, 2008)
The INFN organised in Trieste, Italy, a Training for Grid Site Administrators (24-28/11/2008) and a Training for Grid Application Developers (29-12/12/2008)
e-NMR grid infrastructure operational (November 2008, eNMR D2.1)
Documentation describing this milestone is available here.
e-NMR annual meeting held in Padova (November 4th, 2008)
Slides of the meeting are available (BMRZ, CERM, BCBR, INFN, Spronk)
e-NMR database model released (July 2008, eNMR D1.1)
Documentation describing the eNMR database model is available here.
Fully functional HADDOCK web server released (June 1st, 2008)
The new HADDOCKing web server with full functionality is now accessible from the following addresses:
http://haddock.chem.uu.nl
http://www.haddocking.org
http://www.haddocking.euThe 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.
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 eNMR toward making the HADDOCK server gridable which will increase our computational capacity in the future.
Biomed Grid School (May, 2008)
The INFN co-organised the Biomed Grid School in Varenna, Italy (12-16/05/2008)
First use cases released (April 2008, eNMR D3.1)
A number of use-cases are now available providing examples on how to run structure calculations on the eNMR grid with CNS or Xplor-NIH or automated assigment with MAPPER. See the WIKI for description and download.
e-NMR software development meeting (April 14-15, 2008, Florence)
A meeting for e-NMR software development was held at CERM.
Advanced NMR workshop From Data to Structures
The Bijvoet-NSR Research Alliance (BNRA), with support from the e-NMR and NMR-Life European projects, organizes an advanced NMR workshop on biomolecular structure determination by NMR and complementary techniques, including SAXS and cryo-EM. The workshop will be held in Utrecht, The Netherlands and starts on May 26th and ends on June 6th. The program combines workshop sessions in the morning with a ‘hands-on’ tutorial program in the afternoon, primarily intended for PhD and master’s students.
The workshop consists of lectures and practical sessions. Topics dealing with analysis, structure determination and validation of biomolecules will be discussed. The acquired knowledge will be directly applied in the practical sessions.
For more information visit the workshop web site.
e-NMR gLite training (Januari 17-18, 2008)
The first e-NMR gLite Training for grid administrators was held at CERM.
A theoretical presentation of the various gLite grid elements was followed by the practical deployment of remote CEs at BMRZ and BCBR sites
- July 3rd, 2008: Presentation at the EU-NMR satellite symposium of the 33rd FEBS Congress & 11th IUBMB Conference in Athens, Greece
- May 12th-16th, 2008: e-NMR was presented at the Biomed GRID school in Varenna, Italy
- January 23rd, 2008: e-NMR was presented at EU-NMR user meeting in Königstein (Frankfurt)
- January 5th, 2008: e-NMR was presented at the NMR-life meeting on "Networking in BioNMR" in Florence
- November 1st, 2007: The e-NMR project officially started.
- November 16th, 2007: The kick-off meeting took place at the BMRZ in Frankfurt.