Gromacs MetaDump was published in the Journal of Cheminformatics
GROMACS MetaDump, a tool for automatic annotation of output files from GROMACS MD simulations, was published in the Journal of Cheminformatics.
αCharges and Mol*VS published in 2023 NAR WSI
The Web Server issue of the Nuclear Acids Research hosts two articles authored by the Structural Bioinformatics research group this year. The first informs about Ondřej Schindler's AlphaCharges (αCharges) web server. This application computes partial atomic charges for more than 200 million protein structures in the AlphaFoldDB database. Each on-demand calculation is completed fast using our SQE+qp empirical charge calculation method. Results can be downloaded or viewed in our Mol* viewer. The full text of the article is openly available here: αCharges: partial atomic charges for AlphaFold structures in high quality.
The second article focuses on an extension of widely adopted Mol* viewer. David Sehnal and his team developed Mol* Volumes and Segmentations (Mol*VS), which adds support for the interactive visualisation of cellular imaging data into Mol*. All entries of the community-recognised repositories EMDB and EMPIAR are ready for visualisation in a web browser. As is David's custom, everything is fast and bandwidth-thrifty, meaning that users can view the results of electron and light microscopy experiments on their smartphones. The full text of the article is openly available here: Mol* Volumes and Segmentations: visualization and interpretation of cell imaging data alongside macromolecular structure data and biological annotations.
