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

Bending in the right direction.

Trevor Siggers1, Tonya Silkov, Barry Honig

  • 1Howard Hughes Medical Institute, Center for Computational Biology and Bioinformatics, Columbia University, 1130 St. Nicholas Avenue, ICRB, Mail Box 200, New York, New York 10032, USA.

Structure (London, England : 1993)
|October 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

Autoimmune non-coding variants perturb transcription factor-cofactor complex assembly linked to enhancer activity.

bioRxiv : the preprint server for biology·2026
Same author

A functional investigation of antibody Fc-FcRn variant binding guided by <i>in silico</i> free energy perturbation methods.

bioRxiv : the preprint server for biology·2026
Same author

Atlas of HIV cis-regulatory elements reveals extensive transcriptional variation across clades, isolates, and within individuals.

bioRxiv : the preprint server for biology·2026
Same author

Proteome-wide prediction of interactions between structured domains and peptide motifs reveals functionally coherent subnetworks.

Proceedings of the National Academy of Sciences of the United States of America·2026
Same author

NF-κB: A Diverse and Multifunctional Transcription Factor in Holozoans.

Molecular biology and evolution·2026
Same author

PrePPI - Structure-based Prediction of Protein-protein Interactomes and Networks.

Journal of molecular biology·2026
Same journal

Identification and structure determination of a type III-Bv CRISPR complex that post-translationally modifies an associated toxin.

Structure (London, England : 1993)·2026
Same journal

Cryo-EM structure of the Arabidopsisthaliana ribosome in translating and non-translating states.

Structure (London, England : 1993)·2026
Same journal

Multifaceted effects of N-glycosylation on amyloidogenic κ light chains in AL amyloidosis.

Structure (London, England : 1993)·2026
Same journal

Near-complete cryo-EM structure of the Klebsiella pneumoniae podophage RAN69 reveals tail fiber-spike interface and a divergent pre-ejectosome.

Structure (London, England : 1993)·2026
Same journal

Saxiphilin is a broad-spectrum toxin sponge for C13-modified saxitoxins.

Structure (London, England : 1993)·2026
Same journal

Cryo-EM structure of YfdQ reveals a widespread family of bacteriophage-associated proteins with shell-like assemblies.

Structure (London, England : 1993)·2026
See all related articles

A new Monte Carlo algorithm successfully models DNA bending based on specific sequences. This method enhances predictions of transcription factor binding sites by accounting for indirect readout effects.

Area of Science:

  • Computational biology
  • Biophysics
  • Molecular modeling

Background:

  • Predicting transcription factor binding sites is crucial for understanding gene regulation.
  • Existing models often struggle to accurately capture sequence-specific DNA conformational changes.
  • Indirect readout mechanisms, where DNA structure influences protein binding, are complex to model.

Discussion:

  • A novel Monte Carlo algorithm is presented for simulating sequence-specific DNA bending.
  • The algorithm's success in describing DNA conformational dynamics is demonstrated.
  • This approach provides a more accurate representation of DNA structure relevant to protein interactions.

Key Insights:

  • The developed Monte Carlo algorithm effectively models sequence-dependent DNA bending.

Related Experiment Videos

  • This advancement improves the understanding of DNA structure in molecular recognition.
  • Accurate DNA bending simulation is key to deciphering protein-DNA interactions.

    • Outlook:

    • The algorithm holds promise for refining predictions of transcription factor binding.
    • Future applications may include drug design and synthetic biology.
    • Further development could incorporate more complex biophysical interactions.