Services for the European Open Science Cloud

EOSC-hub WeNMR

WeNMR - Structural biology in the cloud - 10 years of experience of using EGI services

Friday, April 24, 2020 - 14:00 to 15:00

Structural biology deals with the characterization of the structural (atomic coordinates) and dynamic (fluctuation of atomic coordinates over time) properties of biological macromolecules and adducts thereof. Gaining insight into 3D structures of biomolecules is highly relevant with numerous applications in health and food sciences, with as current example unraveling the structural details of Sars-Cov2 in the COVID-19 pandemic.

Since 2010, the WeNMR project has implemented numerous web-based services to facilitate the use of advanced computational tools by researchers in the field, using the grid computational infrastructure provided by EGI. These services have been further developed in subsequent initiatives under the H2020 EGI-ENGAGE West-Life project and the BioExcel Center of Excellence for Biomolecular Computational Research. The WeNMR services are currently operating under the European Open Science Cloud with the H2020 EOSC-Hub project, with the HADDOCK portal sending >10 millions jobs and using ~2700 CPU years  per year. In this talk, Alexandre will summarize 10 years of successful use of e-infrastructure solutions to serve a large worldwide community of users (>16’000 to date), providing them with user-friendly, web-based solutions that allow to run complex workflows in structural biology. I will illustrate this with details of the HADDOCK service and how we could increase our capacity to serve COVID-related projects.

HADDOCK Workshop

Wednesday, December 18, 2019 - 09:00 to Thursday, December 19, 2019 - 18:00

HADDOCK workshop on information – driven modelling of biomolecular complexes”, taking place in Coimbra in the 18 and 19 of december 2019, has been credited with 0.76 UC by “Colégio de Biologia Humana e Saúde da Ordem dos Biólogos”.

Advanced Gromacs, HADDOCK and PMX workshop

Wednesday, October 9, 2019 - 12:00 to Friday, October 11, 2019 - 13:00

The worshop will introduce HADDOCK, (High Ambiguity Driven protein-protein DOCKing) which is an information-driven flexible docking approach for the modeling of biomolecular complexes, and PMX which is a service for users who need to do free energy calculations. PMX utilizes the Gromacs classical molecular dynamics simulation engine to perform calculations at the background. The workshop also covers advanced usage of Gromacs itself in particular on HPC environment.

Lecture and HADDOCK tutorial as part of the CECAM BImMS 2019 meeting

Saturday, October 5, 2019 - 09:00 to Sunday, October 6, 2019 - 13:00

The school is co-organized with the COST Action MuTaLig. The COST action will support 30 selected applicants to partially cover their travel and living expenses. The selection of the COST supported trainees will be carried out by the a Scientific Commission composed by four members of the COST Action, involved in computational research activities. The grant will be sent only after following the training school, according to the rules of the COST Vademecum (Part B).

More details in the web page: https://www.cecam.org/workshop1803/

How to apply bioinformatics to metallo-proteins

Tuesday, February 12, 2019 - 09:00 to Friday, February 15, 2019 - 18:00

As part of the periodic National School for Bioinorganic Chemists organized by the Italian Chemical Society, the present activity aims at training PhD students and post-doctoral fellows in the use of advanced computational methods for the investigation of metal-binding biological systems. In particular, the use of on-line database resources in conjunction with state-of-the-art software for the simulation of the structure and dynamics of metal-binding proteins is addressed.

Synergy of experiment and computation in quantitative systems biology

Sunday, June 23, 2019 - 18:00 to Friday, June 28, 2019 - 09:00

Computational methods and biophysical experiments have advanced rapidly in parallel over recent decades, and are now applied widely to gain molecular-level insights on biological systems. The vast majority of biophysical methods report on the behavior of populations of molecules or on the properties of states of a system. Yet a quantitative understanding of biological systems requires a molecular-level description of phenomena that is generally unobtainable from measurements carried out in bulk. Computations carried out on single macromolecules do not necessarily reflect the statistical nature of molecular behaviors or systems that is captured by experiment. Yet computational approaches can be highly valuable for predicting and interpreting experimental results, and for designing critical experiments to test hypotheses. 

EBI Hinxton - Joint Instruct-ERIC/CAPRI Workshop on Integrated Modelling of Protein-Protein Interactions

Monday, April 1, 2019 - 08:30 to Tuesday, April 2, 2019 - 16:30

CAPRI (Critical Assessment of Predicted Interactions) is a community wide experiment designed to test methods for predicting the structure of macromolecular complexes based on the known structure of their components.

The meeting program will include an overview of the performance of protein docking and scoring procedures obtained for targets evaluated since the spring of 2013. It will also feature several plenary lectures by prominent scientists, as well as talks by the best CAPRI performers, and/or groups developing innovative computational approaches. CAPRI groups selected for oral representations will be notified, once the predictions for all outstanding targets have been completed.

Get the latest update on the current status of computational procedures for modeling protein-protein interactions and the association of proteins with other macromolecules from this 7th CAPRI evaluation meeting. For more information - http://www.ebi.ac.uk/msd-srv/capri/

EMBO practical course on Practical Integrative Structural Biology

Sunday, November 3, 2019 - 17:00 to Saturday, November 9, 2019 - 22:00

Characterizing the structure of macromolecular complexes is crucial for understanding their function. For many complexes, however, solving their structure using a single structural biology technique is very challenging. Integrative structural biology combines different experimental techniques with computational modeling to build structural models of such challenging complexes.

Application of integrative structural biology requires an in-depth understanding of both different experimental approaches and computational modeling. To provide advanced training in such a highly interdisciplinary skill set, this EMBO Practical Course will teach how to interpret data from major structural biology techniques and how to integrate this data using computational methods. The course location at the Hamburg Unit of the European Molecular Biology Laboratory and the Center for Structural Systems Biology on the DESY campus will provide on-site synchrotron SAXS and MX beamlines for training. Hands-on practicals will use a well-studied model system, for which data from all main structural biology techniques are available.

INSTRUCT training course: Advanced methods for the integration of diverse structural data, Florence IT

Monday, February 19, 2018 - 12:30 to Friday, February 23, 2018 - 14:30

This Practical Course co-organized by INSTRUCT and West-Life will introduce and make extensive use of user-friendly e-Science portals to facilitate the adoption of the methods and techniques by the participants in their everyday work. In particular, we will exploit the web-based, cloud-enabled services of the WeNMR and West-Life e-infrastructures, also in collaboration with the European Grid Initiative (EGI). West-Life is a H2020 EU project.

The hands-on sessions will allow the students to try the methods on either pre-packaged or their own research data.

The course will address state-of-the-art tools and facilities.

Topics:

  • Model building in electron maps
  • Cryo-EM analysis of biomolecular assemblies
  • Comparison and integration of techniques
  • Data-driven docking
  • Information-driven docking
  • Design of small-molecule ligands
  • Bio-SAXS
  • MD refinement and simulations
  • SAXS and NMR methods for IDPs
  • Structure validation