Contact Molecular Surface
Measure contact molecular surface across a protein interface.
Results
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Method & evidence
Compute target and binder contact molecular surface for explicit chain groups and compare residue-level contributions.
Scope & limitations
- The input must already be a bound complex; the method does not dock separate structures.
- PDB insertion codes are not supported because residues are identified by chain and integer residue number.
Interpreting results
- CMS measures geometric packing in the submitted conformation; it is not binding affinity or free energy.
- Compare normalized values only across consistently prepared complexes and identical chain-scope policy.
- Inspect high-contributing residues in structural context before prioritizing mutations.
References
Input requirements & outputs
Input checks
- One bound-complex PDB structure per selected row
- Explicit disjoint one-character binder and target chain IDs
- Up to 8 structures, 2 MiB per PDB, and 8 MiB per Job
Expected results
- Interface CMS values — Compare target, binder, maximum-possible, and normalized target CMS.
- Per-residue contributions — Inspect residue CMS values whose sums reconstruct each reported total.
- Chain and residue context — Keep the selected chain groups and contributing residues next to each interface value.
