Voronota-LT benchmark

## Benchmarking with comparison to vanilla Voronota

### Input and output data

Voronota-LT command-line tool was benchmarked on a diverse set of structures of multi-chain biological assemblies downloaded from the Protein Data Bank.

All the 14861 used PDB IDs, and the summary values obtained after processing their first biological assemblies, are in the table “pdb_ids_sizes_correlations_times.tsv”.

All the encountered inter-chain interfaces and their areas are liste in the table “pdb_ids_chain_chain_areas.tsv”.

### Plots

#### Running time

Below are plots summarizing the time efficiency of constructing contacts using vanilla Voronota (Vanilla-AW) and various modes of Voronota-LT (LT-*). Total running times (including input, computation and output routines) were used for every plot. All the software was compiled and run on the same machine (20-core Intel(R) Xeon(R) Silver 4210R CPU @ 2.40GHz, Ubuntu Linux 23.04, GCC g++ compiler version 12.3.0).

#### Summary of correllations of areas computed by Voronota-LT and vanilla Voronota

Below are the Pearson correlation coefficients between differently produced sets of areas for every input structure. For a more convenient display, the values were rounded up to four significant digits.

    x                                                        y                                                        min_Pearson_cor_coeff  average_Pearson_cor_coeff
    Voronota-Vanilla-AW atom-atom area                       Voronota-LT-Radical atom-atom area                       0.9609                 0.9843
    Voronota-Vanilla-AW atom-atom area                       Voronota-LT-AW atom-atom area                            0.999                  1
    Voronota-Vanilla-AW atom-atom area, using uniform-radii  Voronota-LT-Radical atom-atom area, using uniform-radii  1                      1
    Voronota-Vanilla-AW residue-residue area                 Voronota-LT-Radical residue-residue area                 0.9947                 0.999
    Voronota-Vanilla-AW SAS area                             Voronota-LT-Radical SAS area                             0.9997                 1

#### Correlation between contact areas computed by vanilla Voronota and Voronota-LT on atom-atom and residue-residue levels

#### Differences between inter-chain interface contact areas computed by vanilla Voronota and Voronota-LT

## Benchmarking with comparison to SBL-Vorlume

### Input and output data

Voronota-LT was also compared with the SBL-Vorlume software from the “Structural Bioinformatics Library”.

The comparison was done for the 12402 PDB IDs that resulted in exactly the same sets of atoms read by both Voronota-LT and SBL-Vorlume.

The input atomic radii for Voronota-LT were the same as the radii assigned by SBL-Vorlume.

The summary values (total volumes, total SASA, calculation times, statistics of per-atom volume and SASA differences) for the used PDB IDs are in the table “volumes_and_sasa_and_calculation_times_in_comparison_with_sbl_vorlume.tsv”.

### Plots

## Comparing tessellation-based vs simple distance cutoff-based identification of interactions in protein-protein interfaces

(a) Tessellation-derived inter-chain interface contacts.

(b) Distance cutoff-derived pairs of atoms in inter-chain interface.

(c) Tessellation-derived pairs of atoms in inter-chain interface.

(d) Histogram of distances between atoms in inter-chain interfaces observed in the processed PDB structures.

(e) Areas and distances of tessellation-derived contacts in inter-chain interfaces observed in the processed PDB structures.