2024bioinformatics group Mittweida
SequenceCEROSENE - color encoding of residues obtained by spatial neighborhood embedding

As a bioinformatics group mainly focused on investigating structural properties and binding modes of proteins on a basis of dozens or hundreds of structures in one study, we found ourselves often stuck to answering rather simple questions, such as: Where is chain X located relative to chain Y? Which residues are observed in the interface? Which residues are involved in ligand binding, and where are major structural rearrangements observed upon binding?

Here, stripping down structure by structure using dedicated molecular viewers is the best choice to address such questions. However, this process is often quite time consuming and tedious. To assist the researcher to carry out her initial (or even brief) study of a given structure, we developed SequenceCEROSENE.

SequenceCEROSENE (pronounced kerosene) produces sequence representations of molecular structures which allow quickly conceiving its general structural characteristics. Using a straightforward approach, a given structure (any complex which is combination of protein, DNA, or RNA chains) is translated into the three-dimensional RGB color space. Thus, translated coordinates result to residue-specific coloring that corresponds to a residue's spatial location. These colors are then used to colorize the corresponding sequence of the molecular chain. Having a molecular structure at hand, color similarity between one or multiple colorized sequences relate to structural proximity.

The SequenceCEROSENE web server allows to generate, download and interact with obtained sequence representations. For more information and an example, please see the Help & Example section.