A worldwide e-Infrastructure for NMR and structural biology

CECAM workshop on "INTEGRATED SOFTWARE FOR INTEGRATIVE STRUCTURAL BIOLOGY"

Event Date: 
Mon, 2012-05-21 13:00 - Wed, 2012-05-23 14:00

I would like to draw your attention to the upcoming CECAM collaboration scientific software development meeting which will take place at the Cosener’s House, Abingdon, Oxfordshire, United Kingdom, May 21, 2012 - May 23, 2012.  You will find below the programme.

For additional information and registration please visit:

   https://eventbooking.stfc.ac.uk/news-events/integratedsoftware-for-integrative-structural-biology

Best regards
Alexandre Bonvin


Structural biologists use a variety of software tools to help their work, from data collection, through the creation of structural models, to finding biological significance in the results. Some of these tools work together well, with seamless data transfer and a consistent user interface. Others do not, often because they have been developed separately, by groups that are part of different subdisciplines of structural biology, e.g. X-ray crystallography and nuclear magnetic resonance spectroscopy.

Now structural biologists are targeting mesoscale structures including the macromolecular machinery of the cell. Increasingly often, they combine different techniques in a single large research project, aiming to create multiscale models. This raises the challenge to software developers of working together to create an integrated and extensible toolset that supports a range of experimental techniques, as well as modelling and simulation methods.

Such a toolset will also allow synergy between researchers beyond planned collaborations, by ensuring for example that a model that has been deposited in a public database can easily be reused within an investigation that is based on complementary techniques.

This workshop will discuss progress towards these goals and challenges along the way. The workshop is timely as there is now a strong drive for structural biologists to look beyond their own subdiscipline. The European ESFRI projects, such as INSTRUCT (http://www.structuralbiology.eu/) and ELIXIR (http://www.elixir-europe.org/), are encouraging multi-disciplinary approaches, and there is also a desire to fit individual experimental results into a systems view of the cell or organism. These scientific drivers must be supported by a suitable software environment. While this is widely recognised, there is as yet no coherent effort in this direction.
 
The problems of working on a multi-disciplinary structural biology project, using a diverse set of software tools, is well known, but it is not clear how to address this problem. The workshop will seek to identify the specific areas where progress can be made, and discuss possible solutions. Questions for consideration include:
* multi-disciplinary software versus data conversion software to transfer between stand-alone packages
* the need for standardisation of data formats or ontologies
* validation and comparison of results between different techniques
* ensuring easy availability and user-friendliness of software

 

Programme:

Monday 21st May

Chair: Dave Stuart

13:00    Alexandre Bonvin    Incorporating low resolution data into the modelling of macromolecular assemblies using HADDOCK
14:00    Johannes Soeding    Using the HH-suite software for sequence searching and homology modelling
15:00 Coffee
15:15    Michael Habeck        Integration of structural data using Bayesian inference
16:15    Marco Biasini        Getting more Biology into Homology Models

Tuesday 22nd May

Chair: Keith Wilson

09:00    Mark Sansom        Multiscale Simulations for Membrane Proteins
10:00    Geerten Vuister        Large-scale analysis, validation and computation of NMR-derived biomolecular structures: lessons for integrative approaches
11:00     Coffee
11:15    Steve Brewer, EGI    Integrated e-infrastructure for integrated software for integrated structural biology: defining the roadmap for collaboration
12:15 Lunch

Chair: Martyn Winn

13:00    Victor Lamzin        TBC
14:00    Arwen Pearson        TBC
15:00    Coffee
15:15    Jose Maria Carazo    TBC
16:15    Antonio Rosato        Integrated Use of Paramagnetic NMR and X-ray for Structural Biology

Wednesday 23rd May

Chair: J-M Carazo

0900    Torsten Herrmann    The UNIO suite for automated liquid and solid-state NMR structure determination
1000    Gerard Kleywegt        the wwPDB/PDBe plans for deposition, annotation and validation of X-ray/NMR/EM structures
1100 coffee
11:15    Ernest Laue            Epigenetic inheritance: Structural studies of Chromatin assembly/disassembly
12:15 Lunch

 

Visit for more information the CECAM workshop site.

Cite WeNMR/WestLife

 
Usage of the WeNMR/WestLife portals should be acknowledged in any publication:
 
"The FP7 WeNMR (project# 261572) and H2020 West-Life (project# 675858) European e-Infrastructure projects are acknowledged for the use of their web portals, which make use of the EGI infrastructure and DIRAC4EGI service with the dedicated support of CESNET-MetaCloud, INFN-PADOVA, NCG-INGRID-PT, RAL-LCG2, TW-NCHC, SURFsara and NIKHEF, and the additional support of the national GRID Initiatives of Belgium, France, Italy, Germany, the Netherlands, Poland, Portugal, Spain, UK, South Africa, Malaysia, Taiwan and the US Open Science Grid."
 
And the following article describing the WeNMR portals should be cited:
Wassenaar et al. (2012). WeNMR: Structural Biology on the Grid.J. Grid. Comp., 10:743-767.

EGI-approved

The WeNMR Virtual Research Community has been the first to be officially recognized by the EGI.

European Union

WeNMR is an e-Infrastructure project funded under the 7th framework of the EU. Contract no. 261572

WestLife, the follow up project of WeNMR is a Virtual Research Environment e-Infrastructure project funded under Horizon 2020. Contract no. 675858

West-Life