ResComm

Automated residue interaction network analysis from PDB files

Advanced: interaction distance thresholds (optional)

ResComm uses Ca–Ca distance cutoffs as proxies for interaction detection (see Methods / Limitations in the manuscript for the rationale and known trade-offs). The defaults below are literature-calibrated and are what the manuscript's validation results use. You may override them here to test sensitivity on your own structure; results computed with non-default values are flagged as such in the report and are not directly comparable to the published validation.

Default 3.5 Å (McDonald & Thornton 1994); allowed range 2.5–5 Å
Default 4.5 Å (Kumar & Nussinov 1999); allowed range 3–8 Å
Default 6.0 Å (Tsai et al. 1999); allowed range 3–10 Å
Default 2.56 Å (Thornton 1981); allowed range 1.8–3.5 Å
Default 8.0 Å (Brinda & Vishveshwara 2005); allowed range 5–12 Å
Reset to defaults
Default parameters: H-bond = 3.5 Å Salt bridge = 4.5 Å Hydrophobic = 6.0 Å Contact = 8.0 Å (all user-adjustable above) | Weighted LPA community detection (50 iter, 10 runs, best Q) | Exact Brandes betweenness centrality | Grid optimization for > 300 residues

Smart Filtering

Water & non-protein entities removed automatically (11 water types)

5 Interaction Types

H-bonds, salt bridges, hydrophobic, disulfides, contacts — thresholds adjustable

Communities

Weighted LPA 10 runs best modularity Q

Exact Centrality

Full Brandes betweenness + composite Hub Score

Sample PDB Files

Download any and upload above:

1CRN Crambin (46 aa) 1UBQ Ubiquitin (76 aa) 1LYZ Lysozyme (129 aa) 1HIV Protease (198 aa) 1AQK ~220 aa