Abstract The arcp URI scheme is introduced for location-independent identifiers to consume or reference hypermedia and linked data resources bundled inside a file archive, as well as to resolve archived resources within programmatic frameworks for Research Objects. Reference Stian Soiland-Reyes and Marcos Cáceres (2018): The Archive and Package (arcp) URI […]
Abstract We introduce a computational toolset, named GROmaρs, to obtain and compare time-averaged density maps from molecular dynamics (MD) simulations. GROmaρs efficiently computes density maps, by fast multi-Gaussian spreading of atomic densities onto a 3-dimensional grid. It complements existing map-based tools by enabling spatial inspection of atomic average localization during […]
The new 2018 European HPC Handbook has been published by ETP4HPC and EXDCI2. With Europe establishing itself as a world-class HPC ecosystem, there has been a new wave of projects and centres of excellence(CoE) initiated to further enhance the capabilities of the ecosystem. The handbook features BioExcel as well as […]
This paper was published in BioRxiv in October 2018. Abstract Understanding molecular recognition of proteins by small molecules is key for drug design. Despite the number of experimental structures of ligand-protein complexes keeps growing, the number of available targets remains limited compared to the druggable genome, and structural diversity is […]
Abstract Recently we published PROtein binDIng enerGY (PRODIGY), a web-server for the prediction of binding affinity in protein–protein complexes. By using a combination of simple structural properties, such as the residue-contacts made at the interface, PRODIGY has demonstrated a top performance compared with other state-of-the-art predictors in the literature. Here […]
Abstract We report the performance of HADDOCK in the 2018 iteration of the Grand Challenge organised by the D3R consortium. Building on the findings of our participation in last year’s challenge, we significantly improved our pose prediction protocol which resulted in a mean RMSD for the top scoring pose of […]