Publications

Below is a list of related publications by the partners of the BioExcel consortium. We strive to publish as Open Access, or to provide green open access preprints where gold open access is not possible. Please let us know if you are unable to access any of our publications.


The Archive and Package (arcp) URI scheme

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 […]


GROmaρs: a GROMACS-based toolset to analyse density maps derived from molecular dynamics simulations

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 […]


Large-scale prediction of binding affinity in protein-small ligand complexes: the PRODIGY-LIG web server.

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 […]