SUBSEQ.BIO
DOCS-SHAPE-COMP

Shape-Comp

Calculate interface shape-complementarity style scores for protein complexes or candidate interfaces.

Overview

  • Ranking predicted binder or protein complex interfaces.
  • Comparing related docked poses or designed interfaces.
  • Checking whether an interface has plausible geometric packing before deeper analysis.

Modes

ModeInput shapeWhen to use it
shape_complementarity
Shape Complementarity Default		 Consumes a folder or output set; useful for batches and pipeline handoffs. Score protein complex structures from the selected input source.

Canonical Job Configuration

These are the fields exposed by the default job configuration for shape-comp. They are also returned by GET /api/v1/program/params?program=shape-comp and submitted as the params JSON object to POST /api/v1/job/submit.

ParameterTypeModesWhat it does
chains_a
Chain Group A		 Text All modes Comma-separated chain IDs for the first side of the interface, for example B or B,C.
Required
chains_b
Chain Group B		 Text All modes Optional comma-separated chain IDs for the second side. Leave empty to use all remaining chains.
result_name
Result Name		 Text All modes Optional output basename. The job form writes JSON and TSV files under /outputs.
pass_through_min_sc
Pass-through Min SC		 Number All modes Optional. Copy successful structures with shape complementarity at or above this value into a filtered output folder.
Range: 0-1
Advanced configuration fields
ParameterTypeModesWhat it does
model
Model		 Integer All modes 1-based model index for multi-model structures.
Default: 1; Range: 1-999
altloc_policy
Alternate Locations		 Text All modes How alternate atom locations are handled before scoring.
Default: Fail; Options: Fail, Highest Occupancy, sc-rs Default
include_hetatm
Include HETATM		 Yes/no All modes Include hetero atoms. The default protein-only behavior matches sc-rs defaults.
Default: false
include_hydrogens
Include Hydrogens		 Yes/no All modes Include hydrogen atoms in the surface calculation.
Default: false
recursive
Recursive Batch		 Yes/no All modes Search subfolders for structures in batch mode.
Default: false
continue_on_error
Continue On Errors		 Yes/no All modes Record per-file failures and keep scoring the rest of a batch.
Default: true

Outputs And Metrics

  • Summary tables and JSON records of interface shape-complementarity metrics.
  • Copied or annotated structures when produced by the selected mode.
  • Shape-complementarity scores reflect geometric fit, not binding affinity.
  • Combine shape metrics with confidence, buried area, hydrogen bonds, clashes, and biological context.

Common Examples

  • Single complex: score chains A and B in one PDB.
  • Batch folder: score many PDB/CIF complex outputs and filter by a minimum score.

Example API params

{
  "mode": "shape_complementarity",
  "chains_a": "A",
  "chains_b": "B"
}

Caveats

  • Correct chain selection and biological assembly matter.
  • Good shape complementarity alone does not prove binding.
  • Missing atoms or poor model geometry can distort scores.

Advanced Submit

Advanced submit is still available for direct program arguments through POST /api/v1/job/submit-advanced. Prefer canonical configuration unless you need exact low-level arguments or are reproducing a known command line.

  • Advanced submit can pass direct chain/interface scoring options for custom batches.
  • Use canonical configuration for standard single-complex and batch scoring.
curl -X POST https://subseq.bio/api/v1/job/submit \
  -H "Authorization: Bearer <api_key>" \
  -F program=shape-comp \
  -F 'params={"mode":"interface_score","structure":"complex.pdb","receptor_chains":"A","binder_chains":"B"}'

Further Reading