Additional file 1: of Proper evaluation of chemical cross-linking-based spatial restraints improves the precision of modeling homo-oligomeric protein complexes
Creators: name: Aljaž Gaber
name: Gunčar, Gregor
name: Pavšič, Miha
Publisher: name: figshare
Year: 2019
Subjects: Biophysics
Biochemistry
Cell Biology
Molecular Biology
Biotechnology
Cancer
Hematology

description: Figure S1. Inter-residue distance distributions an Intra- and Inter-subunit EUCs distributions. b Distribution distance increases when using SASDs over EUCs for Intra- and Inter-subunit alternatives. Median values were calculated from kernel density estimates [20]. Figure S2. a-c Effect of threshold distance on assignation when using EUCs. The total values obtained with each threshold are shown in header row and column, while the body of the heatmap shows the proportions of combinations. Values in parentheses represent the relative proportion of assignations obtained using a lower threshold, excluding Non-accessible. In row headers, Amb. stands for Ambiguous and Non-acc. Stands for Non-accessible. Figure S3. Distribution of distance differences between both Inter-subunit alternatives in recreated initial structures. Figure S4. Comparison of simulated cross-links with experimental data (PDB: 1F05). For each scoring function, the precision obtained with experimental cross-links, all possible cross-links and average precision obtained from bootstrapped dataset at 1, 5, 10, and 20%. a Comparison of Oblivious and Normal scoring functions. b Comparison of scoring options All, Only best and Non-Intra applied to Normal-oriented and Normal-stringent scoring functions. c Comparison of symmetry imposing scoring functions Symmetry-matched and Symmetry-difference with Normal scoring functions. Figure S5. Comparison of simulated cross-links with experimental data (PDB: 1IRI). For each scoring function, the precision obtained with experimental cross-links, all possible cross-links and average precision obtained from bootstrapped dataset at 1, 5, 10, and 20%. a Comparison of Oblivious and Normal scoring functions. b Comparison of scoring options All, Only best and Non-Intra applied to Normal-oriented and Normal-stringent scoring functions. c Comparison of symmetry imposing scoring functions Symmetry-matched and Symmetry-difference with Normal scoring functions. Figure S6. Comparison of simulated cross-links with experimental data (PDB: 2PSN). For each scoring function, the precision obtained with experimental cross-links, all possible cross-links and average precision obtained from bootstrapped dataset at 1, 5, 10, and 20%. a Comparison of Oblivious and Normal scoring functions. b Comparison of scoring options All, Only best and Non-Intra applied to Normal-oriented and Normal-stringent scoring functions. c Comparison of symmetry imposing scoring functions Symmetry-matched and Symmetry-difference with Normal scoring functions. Figure S7. Comparison of simulated cross-links with experimental data (PDB: 4MZV). For each scoring function, the precision obtained with experimental cross-links, all possible cross-links and average precision obtained from bootstrapped dataset at 1, 5, 10, and 20%. a Comparison of Oblivious and Normal scoring functions. b Comparison of scoring options All, Only best and Non-Intra applied to Normal-oriented and Normal-stringent scoring functions. c Comparison of symmetry imposing scoring functions Symmetry-matched and Symmetry-difference with Normal scoring functions. Table S1. Comparison of average precisions of scoring functions Normal-oriented, Normal-stringent, Symmetry-matched, and Symmetry-difference. (PDF 366 kb)