Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Experiment Videos

An adaptive dynamic programming algorithm for the side chain placement problem.

Andrew Leaver-Fay1, Brian Kuhlman, Jack Snoeyink

  • 1UNC-Chapel Hill, Chapel Hill, NC 27514, USA. leaverfa@email.unc.edu

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing
|March 12, 2005
PubMed
Summary
This summary is machine-generated.

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Deep learning based design of buried hydrogen bond networks with HBDesigner.

bioRxiv : the preprint server for biology·2026
Same author

De novo masking domains that gate TNF-family ligand assembly and activity.

bioRxiv : the preprint server for biology·2026
Same author

Intensity modulation of trichromatic split fluorescent proteins for live cell mapping.

Cell reports methods·2026
Same author

Enhancing Enzymatic Bioconjugation Efficiency via Computer-Based Installation of a Substrate Recruitment Domain.

Bioconjugate chemistry·2026
Same author

Enhancing ML-based binder design with high-throughput screening: a comparison of mRNA and yeast display technologies.

bioRxiv : the preprint server for biology·2026
Same author

De novo design of protein binders that target DELE1 to inhibit the mitochondrial stress response.

bioRxiv : the preprint server for biology·2026
Same journal

Trust, Reproducibility, and Progress: The Roles of Independent Blind Prediction and Assessment and Benchmarking in Computational Biology.

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing·2026
Same journal

The Evolving Cyberinfrastructure at the National Institutes of Health to Support Data and AI in Biomedical Research.

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing·2026
Same journal

Applications of AI & ML in Biomanufacturing of Cell and Gene Therapies.

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing·2026
Same journal

AI for Health: Leveraging Artificial Intelligence to Revolutionize Healthcare.

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing·2026
Same journal

Workshop Introduction: Advances of AI Methods in Single Cell Spatial Omics.

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing·2026
Same journal

DRIVE-KG: Enhancing variant-phenotype association discovery in understudied complex diseases using heterogeneous knowledge graphs.

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing·2026
See all related articles

This study introduces a dynamic programming method for protein design, efficiently searching side chain conformations. The new approach balances accuracy and speed, enabling better protein redesigns like ubiquitin

Area of Science:

  • Computational Biology
  • Protein Engineering
  • Bioinformatics

Background:

  • Larger rotamer libraries improve protein design by sampling side chain conformations finely.
  • However, these libraries significantly slow down computational search algorithms.

Purpose of the Study:

  • To develop a more efficient algorithm for the side chain placement problem in protein design.
  • To balance the resolution of rotamer sampling with computational speed.

Main Methods:

  • A dynamic programming approach was adapted for side chain placement.
  • The algorithm selectively uses high or low rotamer resolution as needed.
  • Error analysis was performed on the approximation introduced by the method.

Main Results:

Related Experiment Videos

  • The developed algorithm efficiently searches side chain conformations.
  • It allows for the redesign of surface residues, demonstrated on ubiquitin's beta sheet.
  • The method provides a way to approximate exact dynamic programming solutions with controllable error.

Conclusions:

  • This dynamic programming solution offers an efficient and accurate method for protein side chain placement.
  • It enables improved protein design by optimizing conformation searches.
  • The approach is applicable to redesigning protein surfaces, enhancing protein functionality.