Bioinformatic Tools

The following online bioinformatic services are available:

AlphaFill is an algorithm based on sequence and structure similarity that “transplants” missing ligands, cofactors and (metal) ions to AlphaFold models or user provided models (both computational and experimental). By adding the molecular context to these protein structures, the models can be more easily appreciated in terms of function and structural integrity. Consequently, the AlphaFill models can be helpful in designing downstream wet-lab experiments and/or computational studies.

The Model Zoo is collaborative effort to bring AI models to the bioimaging community from AI4Life. Integrated with various tools, the Zoo allows modelling with BioEngine to explore datasets and imaging.

DSSP (Dictionary of Secondary Structure in Proteins) is an algorithm designed to standardise secondary structure assignment based on atomic coordinates. DSSP does not predict secondary structure. DSSP provides an elaborate description of the secondary structure elements in a protein structure, including backbone hydrogen bonding and the topology of β-sheets.

  • 3D Bionotes

    Annotates a structure with information from many biomedical databases.

  • MetalPDB

    Collects and allows access to the knowledge on metal sites in biological macromolecules, starting from the structural information contained in the Protein Data Bank (PDB)