USW
Structural BiologyStructure PredictionMediumSeed

Predict a transient protein–protein complex

Predict the structure of a weakly-bound complex and validate the interface against crosslinks.

Dr. Ahmed Rahimi
Computational Structural Biology
Accurate prediction of protein complexes
Nature · 2024
~4 h
registered 2025-08-19
complexinterfacevalidation

End goal

Predict the interface with DockQ ≥ 0.49 (medium quality).

Overview

The agent predicts the complex, ranks models by interface confidence, and checks consistency with experimental crosslinking restraints.

Tools allowed

1
AlphaFold 3·HPC

Workflow

1-step protocol

Each step is verified against the scientist's targets. Open any simulation to test it live.

  1. 1

    Predict & rank

    Step 1 / 1

    Predict complex models and rank by interface confidence.

    Protocol

    1. aPredict complex.
    2. bRank by ipTM.
    3. cCheck crosslink satisfaction.

    Targets

    Interface quality≥0.49DockQ
    Expected output

    A top model with interface quality metrics.

    Simulations · click to test