This tutorial will demonstrate the use of HADDOCK for predicting the structure of a protein-protein complex from NMR chemical shift perturbation (CSP) data. Namely, we will dock two E. coli proteins involved in glucose transport: the glucose-specific enzyme IIA (E2A) and the histidine-containing phosphocarrier protein (HPr).
The structures in the free form have been determined using X-ray crystallography (E2A) (PDB ID 1F3G) and NMR spectroscopy (HPr) (PDB ID 1HDN). The structure of the native complex has also been determined with NMR (PDB ID 1GGR).
These NMR experiments have also provided us with an array of data on the interaction itself (chemical shift perturbations, intermolecular NOEs, residual dipolar couplings, and simulated diffusion anisotropy data), which will be useful for the docking. For this tutorial, we will only make use of inteface residues identified from NMR chemical shift perturbation data as described in Wang et al, EMBO J (2000).
OPENCoastS is an online service (https://opencoasts.ncg.ingrid.pt/) that assembles on-demand circulation forecast systems for selected coastal areas and keeps them running operationally for a period defined by the user. This service generates daily forecasts of water levels and vertically averaged velocities over the region of interest for 48 hours, based on numerical simulations of all relevant physical processes. Presently, all forecasts are made with the model SCHISM (http://ccrm.vims.edu/schismweb/) and are supported by the computational resources from INCD - Infraestrutura Nacional de Computação Distríbuida (https://www.incd.pt), a node of the EGI - European Grid Infrastructure (https://www.egi.eu). Access to the service is granted through a registration procedure, and is obtained after acceptance of the registration by the OPENCoastS user support. OPENCoastS is jointly developed and maintained by LNEC - Laboratório Nacional de Engenharia Civil (LNEC - http://www.lnec.pt), LIP - Laboratório de Instrumentação e Física Experimental de Partículas (LIP - https://www.lip.pt), CNRS-LIENS - Centre National De La Recherche Scientifique - LIttoral ENvironnement et Sociétés (CNRS-LIENS - https://lienss.univ-larochelle.fr) and Universidad de Cantabria (UC - https://web.unican.es).
EIDA is the European Integrated Data Archive insftrastructure within ORFEUS to provide access to seismic waveform data and related metadata in European archives. EIDA has been stablised in 2013. EPOS-ORFEUS Competence Center works on new federated seismologiical services for EIDA. The presentation slides introduced the new Authentication and Authorization for EIDA developed by the CC. The two presentations were given in EGU 2019 conference, April 10th 2019, Vienna, and in EPOS Seismology Meeting, May 7th 2019, Potsdam, respectively.
The main goal of the EOSC-hub project is to synergize the services and infrastructures from major European providers including EGI and EUDAT, enabling researchers to freedom of choice of the services, data and infrastructure necessary for their work. Users from many communities have reported interest in being able to use resources provisioned by these 2 infrastructures simultaneously in a transparent fashion, i.e.:
using single sign on mechanisms between infrastructures
being able to transparently transfer data between infrastructures
EOSC-hub WP6 has been endeavoring to enable transparent data access between the infrastructures. The main data management components in EGI and EUDAT are respectively, EGI-DataHub based on Onedata platform and B2SAFE/B2STAGE based on iRODS. Currently no transparent mechanisms allowing users to move data between these infrastructures exists, the only options are manual transfers using such tools as GridFTP.
These two demo videos present the managment of data transfer across EGI, EUDAT, INDIGO data and compute services.
The first demo video shows the how data can be transparently moved from EGI to EUDAT. It divided into 4 sections:
Registration of B2STAGE storage in EGI-DataHub
Creation of dsata space in EGI-DataHub supported by the B2STAGE storage
Upload of some data to the data space
Data access from GUI and command line
The second demo video presents import of existing data from EUDAT to EGI. The demo is divided into the following 4 sections:
Registration of B2STAGE storage in EGI-DataHub
Creation of data space in EGI-DataHub supported by the B2STAGE storage from which existing data is imported to EGI-DataHub
Access of data from B2STAGE using EGI-DataHub user interface
Automatic discovery of new data added on the B2STAGE storage
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.
The MEDCOAST congress in Marmaris (Turkey) is the fourteenth event of the biennial series that was started in 1993 for contributing to coastal and marine sciences, engineering, management and conservation particularly in the Mediterranean and the Black Sea. Since the first event in 1993 (Antalya
IT Service Management is a discipline that helps provide services with a focus on customer needs and in a professional manner. It is widely used in the commercial and public sectors to manage IT services of all types, but current solutions are very heavyweight with high barriers to entry.
T Service Management is a discipline that helps provide services with a focus on customer needs and in a professional manner. It is widely used in the commercial and public sectors to manage IT services of all types, but current solutions are very heavyweight with high barriers to entry.
EOSC-hub receives funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 777536.