Supplementary data for structure-conditioned amino-acid couplings

This dataset contains supplementary data for the work "Structure-conditioned amino-acid couplings: how contact geometry affects pairwise sequence preferences" and includes two files: a spreadsheet listing the CASP models used for structure evaluation and an archived directory containing the structure and energy files that make up "DB200K", the main dataset of interaction motifs and their structure-conditioned energies used in the published work. The spreadsheet, "CASP-models.xlsx", lists the CASP round (9, 10, etc.), target name, model ID, and GDT_TS score for each model included in the structure evaluation experiment (see Fig. 7 in the published work). All information was collected from the CASP website, predictioncenter.org. See the "CASP model evaluation" section in the Methods section of the published work for more information. The archived directory, "DB200K.tar.gz", contains the structures and structure-conditioned energies of 200,002 inter-residue contact motifs. Each motif has a structure and set of structure-conditioned energies for each of the three motif sizes considered in the published work: 1x1, 3x3, and 5x5. For each motif of each size, there are two corresponding files, both indexed by the motif size, PDB ID, and position pair (chain and residue numbers according to the PDB file). One file is a PDB file containing the motif's structure and the other is a text-based file listing the 400 structure-conditioned energies of the motif's interacting residue pair. Each of the 400 energies is indexed by the pair of three-letter amino-acid codes it corresponds to. The residue positions in the PDB file match those listed in the energy file. For details on how this database's contacts were selected, see the "Contact database creation" section in the Methods section of the published work; for details on how these energies were computed, see the "Structure-conditioned potentials" section.