biomolecular DOCKing). By experimental
data and predictions – known as
factoring
submitting in
‘Ambiguous
Interaction Restraints’, the software allows users to examine how molecules can combine, forming structures or ‘complexes’ by theoretically ‘docking’. This process is also
integral to modern
power,
the computations to
duration may
the medicine.
Predicting the mode of interaction at the molecular level is critical to anticipating the function of drug candidates, as their effectiveness may depend on how they attach themselves to specified molecular targets like proteins.
capabilities of overstretched in-house servers, deemed unviable. To address this scenario, in which less well-resourced
scientists
could become marginalised in a hierarchy of HPC elitism, an EU project called WeNMR (Worldwide
e-Infrastructure
for NMR and Structural biology) has been launched, with
Bonvin
“The role of biomolecules is very important to human biology, since they define functions and communication within our bodies”
Despite the availability of many such tools, researchers find their progress
inhibited by inadequate IT resources or a lack of experience in dealing with complex software. Without sufficient processing
An overview of WeNMR NMR Cross-linking MS B 1H D2O
H/D Exchange H
D D
D EPR, FRET cryo-EM, SAXS w -nmr
Mutagenesis +
Titrations A RDC, PCS Bioinformatics
EFRGSFSHL EFKGAFQHV
LFRLTWHHV EFEPSYPHI
coordinator. “WeNMR builds
Grid as on its grid
computing, making use of European
Initiative usage of the (EGI)
resources,” he details. “This is the collective
geographically
disparate IT assets, combined to achieve a common research goal – in this case, progress in molecular biology”. A three year venture,
the project aims to unite
complementary research teams within a virtual research community at a global level. To aid them, the initiative provides an
integrated, streamlined (which supports HADDOCK), platform to provide
an interface assisting with computational analysis and modeling. The platform is
not exclusive to NMR specialists, and also aims
to engage those conducting work
using small-angle x-ray scattering (SAXS), and to form relationships with other branches of the life sciences, which diversify the usage of the grid. Grid computing was historically developed
by CERN in Geneva. Consequently, it has made
a formidable contribution to
discoveries like the Higgs Boson, but this early precedent ensured that grid usage was initially, and continues to be, dominated by physics.
“However, “We’ve in over time,
disciplines have started moving in,” says Bonvin.
begun to combine the life sciences.” the
power of grid computing with numerous applications
To
calculate the 3D structures of molecules using NMR, scientists must repeat complex calculations potentially thousands of times – hence the necessity to accelerate the time- consuming process. A critical goal for the project has thus been to develop a user- friendly gateway or online
‘portal’ for
researchers to access the grid. The system allows them to input and upload data from their experiments, which are processed on the grid. Once analysis
is complete, the
results are returned to the researchers who usually deposit them into public digital knowledge repositories. The project offers support and training to novices, providing a hub around which expertise and knowledge can be shared online for the benefit of the collective.
www.projectsmagazine.eu.com 17
of be
significantly lengthened, or, if restricted
limited
other
15N
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