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

RosettaDesign server for protein design.

Yi Liu1, Brian Kuhlman

  • 1Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA.

Nucleic Acids Research
|July 18, 2006
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

Correction to 'New origin firing is inhibited by APC/CCdh1 activation in S-phase after severe replication stress'.

Nucleic acids research·2026
Same journal

VeloRM: disentangling pre- and post-splicing RNA modification dynamics at single-cell resolution.

Nucleic acids research·2026
Same journal

Accessibility of telomeric overhangs to stabilizing small-molecule ligands.

Nucleic acids research·2026
Same journal

Multivalent interactions mediate SNAIL transcription factor stimulation of the nucleosome deacetylase activity of the CoREST complex.

Nucleic acids research·2026
Same journal

Genome-wide mapping of DNA G-quadruplexes in Trypanosoma brucei chromatin reveals enrichment in coding regions and transcription start sites.

Nucleic acids research·2026
Same journal

Correction to 'The Gene Ontology knowledgebase in 2026'.

Nucleic acids research·2026
See all related articles

The RosettaDesign server generates optimized amino acid sequences for protein structures. This computational tool aids in protein design and stabilization by predicting low-energy sequences.

Area of Science:

  • Computational Biology
  • Protein Engineering
  • Structural Bioinformatics

Background:

  • Protein structure dictates function.
  • Designing novel proteins or stabilizing existing ones requires precise amino acid sequence selection.
  • Computational methods can predict sequence-structure-energy relationships.

Purpose of the Study:

  • To introduce the RosettaDesign server for predicting low-energy amino acid sequences for target protein structures.
  • To provide a user-friendly web server for protein sequence design based on backbone coordinates.

Main Methods:

  • Utilizes the RosettaDesign module, employing Monte Carlo optimization and simulated annealing.
  • Searches for amino acid sequences that exhibit favorable packing and hydrogen bonding interactions with the target protein backbone.

Related Experiment Videos

  • Input: target protein backbone coordinates and specified residues for design. Output: designed sequences, coordinates, and energies.

    • Main Results:

    • The RosettaDesign server successfully identifies low-energy amino acid sequences for given protein structures.
    • The server returns comprehensive design outputs including sequences, coordinates, and calculated energies.
    • RosettaDesign has demonstrated experimental validation and application in protein stabilization and novel protein design.

    Conclusions:

    • RosettaDesign is a validated computational tool for protein sequence optimization.
    • The server facilitates the design of stable and functional protein sequences.
    • This approach has significant implications for protein engineering and synthetic biology.