Interface scope
Binder and target chain groups
Choose non-overlapping PDB chains already positioned in one bound complex.
Analysis method
Run Contact Molecular Surface online
Measure contact molecular surface across a protein interface
Compute target and binder contact molecular surface for explicit chain groups and compare residue-level contributions.
Prepare
Bound protein-complex structures
Use a Structures Dataset whose PDB files contain both binder and target chains.
- 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
Binder chains
ATarget chains
BHow the analysis starts
Choose a Project, open a compatible Dataset, then select the rows you want to analyze. Ubi will open this method with the compatible controls and column mappings ready to review.
Configure the scientific method
These controls appear in the Dataset analysis panel, where values can be checked against the actual input before the run starts.
Binder-side contributions
Included by default
Report binder CMS and residue contributions in addition to the target-side values.
Normalization
Maximum-possible target CMS
Compare target CMS with its geometric upper bound for a normalized packing measure.
Review results as scientific outputs
Results open with the figures, structures, sequences, and metrics needed to answer the scientific question. Downloadable files remain available for downstream analysis.
How to interpret the result
- 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.
1
Interface CMS values
Compare target, binder, maximum-possible, and normalized target CMS.
2
Per-residue contributions
Inspect residue CMS values whose sums reconstruct each reported total.
3
Chain and residue context
Keep the selected chain groups and contributing residues next to each interface value.
Continue your analysis
Use a complementary method on the same Project data.
Method scope and 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.
- Contact molecular surface measures packing geometry, not binding affinity or free energy.
