MOLEonline was published in Bioinformatics
MOLEonline, a tool designed to detect and analyse channels (pores and tunnels) within protein structures, was published in the Bioinformatics journal.
Gromacs MetaDump was published in the Journal of Cheminformatics
The volume of molecular dynamics simulation data shared through public repositories is rapidly increasing; however, fragmentation across several independent repositories, each using different dataset descriptions and metadata schemas, hinders the effective reuse of these data.
To address this, the Structural Bioinformatics research group developed GROMACS MetaDump, a tool for automatic annotation of output files from GROMACS MD simulations. It generates machine-readable metadata from simulations by extending the functionality of the standard GROMACS tool (gmx dump). GROMACS MetaDump primarily utilises the input simulation file (.tpr) and can optionally be enriched with annotations from topological and structural files (.top, .gro).
GROMACS MetaDump was recently published in the Journal of Cheminformatics. Its article is titled Gromacs MetaDump: a tool for extracting GROMACS simulation metadata.
Gromacs MetaDump is available at https://gmd.ceitec.cz/.
