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Related Experiment Video

Updated: Feb 12, 2026

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins
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BBK* (Branch and Bound Over K*): A Provable and Efficient Ensemble-Based Protein Design Algorithm to Optimize

Adegoke A Ojewole1,2, Jonathan D Jou1, Vance G Fowler3

  • 11 Department of Computer Science, Duke University , Durham, North Carolina.

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
|April 12, 2018
PubMed
Summary

BBK* is a novel computational protein design algorithm that efficiently approximates binding affinity for numerous sequences. This breakthrough accelerates protein design and enables previously intractable large-scale designs.

Keywords:
OSPREYmolecular ensemblespredicting binding affinityprotein designstructural biologysublinear algorithms.

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Area of Science:

  • Computational biology
  • Biophysics
  • Protein engineering

Background:

  • Computational protein design (CPD) aims to find sequences with favorable binding free energy.
  • Improving CPD accuracy relies on ensemble-based design, continuous flexibility, and provable accuracy guarantees.
  • Existing methods using these principles are computationally expensive single-sequence (SS) algorithms.

Purpose of the Study:

  • Introduce BBK*, a new CPD algorithm addressing the computational cost of accurate design.
  • Develop a multisequence (MS) bound to efficiently approximate binding affinity for many sequences.
  • Enable provable, ensemble-based CPD in sublinear time with respect to the number of sequences.

Main Methods:

  • Developed the BBK* algorithm featuring a novel multisequence (MS) bound.
  • BBK* computes a single provable upper bound for binding affinity (Ka) across combinatorial sequences.
  • Avoids single-sequence (SS) computation for suboptimal sequences, achieving sublinear time complexity.

Main Results:

  • BBK* successfully identifies tightest-binding sequences in 204 protein design problems.
  • Approximated Ka for up to 105-fold fewer sequences compared to exhaustive methods.
  • Achieved up to 1982-fold speedup in approximating Ka for 51 protein-ligand problems versus state-of-the-art.

Conclusions:

  • BBK* is the first provable, ensemble-based CPD algorithm with sublinear time complexity.
  • Accelerates existing provable protein design tasks.
  • Enables efficient execution of protein designs previously too computationally demanding.