In September’s Nature Methods the project issued an invitation to the entire biomolecular Nuclear Magnetic Resonance community to participate in a large scale test of modern computing algorithms. This community-wide “contest” will potentially improve efficiency, reproducibility and reliability of NMR structure determination. eNMR will be using the Enabling Grids for E-sciencE infrastructure to power their analysis.
NMR spectroscopy is important in many different areas of science and is often used to determine the structure of complex molecules. The technique is particularly useful in biological sciences as it can predict the three dimensional structure of macromolecules in solution, including substances such as proteins and DNA that are key to understanding how the human body works. The analysis, however, is labour intensive and automation would accelerate the pace of research, helping scientists to identify molecules more quickly.
“Insight into the shape of biomolecules is the starting point for designing new drugs,” says Alexandre Bonvin, member of the eNMR project and one of the authors of the paper. “If we can improve this technology, it will help researchers in structural biology to be more productive. This could help shorten the whole process of designing new drugs.”
The small molecule ABT-737, for example, was found by screening a chemical library with NMR-based techniques. The discovery of ABT-737 was covered in the 2005 Nature paper “An inhibitor of Bcl-2 family proteins induces regression of solid tumours,” as a promising cancer fighting compound. (Though it has not, as of yet, been marketed.)
The eNMR project has worked to improve computational methods used for automation since late 2007, using EGEE’s computational resources to calculate molecular structures from NMR data. Their next step is to involve all interested stakeholders in their efforts. Through this challenge – called “Critical Assessment of automated Structure Determination of proteins by NMR” or CASD-NMR – the team invites laboratory researchers to submit molecules (technically the spatial coordinates of the atoms in the molecule with their associated NMR data) to help improve the algorithms used by the global eNMR team.
The CASD-NMR challenge will help computer scientists to automate NMR calculations and test them against blind datasets. The eNMR project and the National Institute of Health’s (NIH) Protein Structure Initiative are providing data for this challenge, and the CASD-NMR team hopes that other researchers will provide additional data sets.
In the future, automation in NMR will allow ‘unsupervised’ results to be accepted by the community as being correct and viable, ready for inclusion in the Protein Data Bank (PDB) straight away. The PDB is a database that stores macromolecular structural data that is freely and publicly available for further research (www.wwpdb.org).
“At this time fully automated methods are not reliable enough to be used blindly; this CASD-NMR experiment will be a valuable tool to see where we stand in automation and improve our methods,” says Bonvin.
CASD-NMR is set up to give the various teams eight weeks to apply automated methods to generate structures at a level of quality comparable to that of structures deposited into the PDB. National Grid Initiatives BigGrid in the Netherlands and IGI/INFN have contributed CPUs to the project so far. An assessment meeting is planned for mid-2010 to look at the results. Data are made available for CASD-NMR participants through the e-NMR project’s webpage (http://www.e-nmr.eu/CASD-NMR).The paper's details:
Notes for Editors
About e-NMR: The main objective of the e-NMR project is to optimise and extend the use of the NMR Research Infrastructures of EU-NMR through the implementation of an e-Infrastructure. The project aims to provide the European biomolecular NMR user community with a platform integrating and streamlining the computational approaches necessary for biomolecular NMR data analysis (e-NMR).
The e-NMR infrastructure is based on the EGEE grid infrastructure and is funded under the 7th framework programme of the European Union (Contract no. 213010 - e-NMR). NMR plays an important role in life sciences (biomolecular NMR), and structural biology in particular, at both European and international levels.
The project will also seeks to:* establish a human collaboration network between the biomolecular NMR and the e-Infrastructure scientific communities
* implement and make available state-of-the-art computational methods.About EGEE:
Press contact: Neasan O’Neil, EGEE Press and Events Manager, +44 (0)79 6281 8712, email@example.com.
Cancer diagnosis: no more needles?
25.05.2018 | Christian-Albrechts-Universität zu Kiel
Less is more? Gene switch for healthy aging found
25.05.2018 | Leibniz-Institut für Alternsforschung - Fritz-Lipmann-Institut e.V. (FLI)
The more electronics steer, accelerate and brake cars, the more important it is to protect them against cyber-attacks. That is why 15 partners from industry and academia will work together over the next three years on new approaches to IT security in self-driving cars. The joint project goes by the name Security For Connected, Autonomous Cars (SecForCARs) and has funding of €7.2 million from the German Federal Ministry of Education and Research. Infineon is leading the project.
Vehicles already offer diverse communication interfaces and more and more automated functions, such as distance and lane-keeping assist systems. At the same...
A research team led by physicists at the Technical University of Munich (TUM) has developed molecular nanoswitches that can be toggled between two structurally different states using an applied voltage. They can serve as the basis for a pioneering class of devices that could replace silicon-based components with organic molecules.
The development of new electronic technologies drives the incessant reduction of functional component sizes. In the context of an international collaborative...
At the LASYS 2018, from June 5th to 7th, the Laser Zentrum Hannover e.V. (LZH) will be showcasing processes for the laser material processing of tomorrow in hall 4 at stand 4E75. With blown bomb shells the LZH will present first results of a research project on civil security.
At this year's LASYS, the LZH will exhibit light-based processes such as cutting, welding, ablation and structuring as well as additive manufacturing for...
There are videos on the internet that can make one marvel at technology. For example, a smartphone is casually bent around the arm or a thin-film display is rolled in all directions and with almost every diameter. From the user's point of view, this looks fantastic. From a professional point of view, however, the question arises: Is that already possible?
At Display Week 2018, scientists from the Fraunhofer Institute for Applied Polymer Research IAP will be demonstrating today’s technological possibilities and...
So-called quantum many-body scars allow quantum systems to stay out of equilibrium much longer, explaining experiment | Study published in Nature Physics
Recently, researchers from Harvard and MIT succeeded in trapping a record 53 atoms and individually controlling their quantum state, realizing what is called a...
25.05.2018 | Event News
02.05.2018 | Event News
13.04.2018 | Event News
25.05.2018 | Event News
25.05.2018 | Machine Engineering
25.05.2018 | Life Sciences