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interface-analysis

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Maps protein-protein and protein-ligand interfaces with Bio.PDB, computing contact residues and buried surface area (BSA). Use when choosing a contact cutoff and stating its rationale (heavy-atom 4-5A vs CA-CA 8A vs a SASA-based definition); deciding a contact list is not an interface and computing buried surface area (dSASA/BSA) instead; distinguishing a genuine biological interface from a crystal-packing artifact; identifying ligand-contact or epitope residues; and computing on the biological assembly rather than the asymmetric unit. Keywords interface, buried surface area, BSA, contacts, NeighborSearch, PISA, crystal packing, epitope, binding site, ShrakeRupley.

When to use

• computing contact residues
• computing buried surface area (BSA)
• choosing a contact cutoff
• distinguishing biological interface from crystal-packing artifact
• identifying ligand-contact residues
• identifying epitope residues
• computing on the biological assembly

When not to use

• reporting contact counts without stating atom set and cutoff
• treating a contact list as an interface
• computing interfaces on the asymmetric unit instead of the biological assembly

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