Project coordinator. IRB is one of the leaders in the MD field and has a strong background in technology-development projects. It is responsible of the development of MD databases such as MoDEL, BigNASim, MDWeb, NAFlex, CNS-DB, Covid19 database, and their associated analysis tools, including the Multiscale Genomics virtual research environment (MuGVRE).
BSC is one of PRACE’s Tier-0 supercomputing centres and it has a deep implication in large-scale Bio-Data projects. It is especially active in the development of computational research infratrucrures like virtual research environments (VRE) and has a strong visibility not only in the IT community, but also in the omics one, as it is a core partner in many personalised medicine initiatives. BSC co-coordinates ELIXIR’s Tools Platform and participates in the definition of Best Practices and guidelines for software development.
KTH is the main developer of GROMACS, the most used MD simulation software. The group has been very active in defining rules for good practices in molecular simulations and has direct access to an extremely large number of users, as well as close interactions and regular joint workshops with other major MD coders . KTH has an influential position in both structural biology and biophysical communities, and it is also responsible for co-developing the RELION software used in cryo-EM.
EMBL-EBI s a global leader in storing, analysing, and disseminating large biological datasets. Hosting over 40 open data resources, including Protein Data Bank in Europe (PDBe), EMBL-EBI empowers researchers to unlock the potential of big data for impactful discoveries. PDBe, a core partner of the worldwide Protein Data Bank (wwPDB), collects, curates, and provides access to the global repository of macromolecular structure models in the Protein Data Bank (PDB). PDBe-Knowledge Base, a community-driven open resource managed by the PDBe team, integrates 3D structure data with structural and functional annotations to establish their biological context for research. As part of PDBe-KB, the 3D-Beacons Network provides unified programmatic access to experimentally determined and computationally predicted protein structures. In collaboration with Google DeepMind, the team developed and maintains the AlphaFold Protein Structure Database, granting open access to over 200 million protein structure predictions. EMBL-EBI’s computational biology research spans sequence analysis, statistical analysis, and data-driven discovery across various fields, from plant biology to mammalian development and disease.
NBD is an SME with a large portfolio of clients including world-leading pharmaceutical and biotechnological companies, but in addition, it has a technological roadmap, which is reflected in the development of the first database of trajectories of toxicity targets with the associated analysis pipeline. NBD provides a link to the industrial world, thus facilitating the tailoring of analysis pipelines to the specific needs of pharmaceutical andbiotechnological companies.
EPFL-CECAM(Centre Européen de Calcul Atomique et Moléculaire) is the headquarter of an international organization that fosters fundamental research on advanced computational methods and their application to forefront challenges in science and technology. CECAM hosts and organizes the most active cycle of training workshops and scientific symposia in Europe and worldwide. This facilitates dialog among different communities in computational science and simulation, also promoting data standards and management policies.
UOXF is not only an excellent representative of the MD simulation community, leading the field of biological membranes simulation, but it has also large experience in creating and maintaining databases of molecular dynamics simulations of membrane proteins. UOXF drives the interaction with the biophysical and medicinal chemistry communities.
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