Fig. 1

Schematic workflow of SequenceCEROSENE and example output shown for transcription promoter CAP (catabolite activator protein, PDB-Id 1cgp [12]). Upon computing the maximum spatial span s _max , the given molecular complex is embedded in a cubic bounding box (a1) and, based on this, translated into RGB color space (a2). Eventually, corresponding sequences are color-coded in accordance to three-dimensional locations of residues (a3) from which structural residue neighborhood can be quickly deduced. For example, interfacial residues between both peptide chains in CAP are located in a region of 22 residues relating to a helix-helix interaction (highlighted by blue box I in (b) and (c)). These residues can intuitively be identified by their common grey-blue coloring in the color encoded sequences. Further, color encoding intuitively reflects that the two dsDNA molecules are comprised by chains C and F as well as D and E. Here, note the reversed color coding of the bound chains, indicating anti-parallel binding. In addition, the DNA binding domain in both peptide chains corresponds to the C-terminal region highlighted by red box B1 respectively B2. Color encoding of the sequences shows that dsDNA D-E and C-F are bound to regions B1 and B2, respectively. Note that in (b) representations of secondary structure elements outside of regions I, B1 and B2 are neglected for visual clarity