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

Predicting interresidue contacts using templates and pathways.

Yu Shao1, Christopher Bystroff

  • 1Department of Biology, Rensselaer Polytechnic Institute, Troy, New York 12180, USA.

Proteins
|October 28, 2003
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

Microstrip Antenna Bandwidth Optimization for RF Microsystems Using Swarm Intelligence and Reinforcement Learning.

Micromachines·2026
Same author

Discovery and validation of key genes and potential mechanisms linked to endothelial cell senescence and carbohydrate metabolism in recurrent spontaneous abortion.

Open medicine (Warsaw, Poland)·2026
Same author

Effects of the traditional nine steaming and nine sun-drying on the bioactivity of traditional Chinese medicine.

Journal of ethnopharmacology·2026
Same author

[Expression of Rho-related BTB domain-containing protein 1 in tongue squamous cell carcinoma and its effect on cell proliferation, invasion, and migration].

Hua xi kou qiang yi xue za zhi = Huaxi kouqiang yixue zazhi = West China journal of stomatology·2026
Same author

ZFP91 restricts RSV replication by driving K48-linked ubiquitination and proteasomal degradation of M2-1.

Cellular and molecular life sciences : CMLS·2026
Same author

Transparent EMI shielding and a thermal insulating optical window based on a randomized metallic mesh and ITO-based coating.

Applied optics·2026
Same journal

Engineered HSP90-MP65 Bivalent Fusion Antigen: A Novel Vaccine Candidate Against Invasive Candidiasis.

Proteins·2026
Same journal

Physics-Based Energy Functions for Computational Protein Design.

Proteins·2026
Same journal

Impact of Stabilizing Osmolytes on the Conformational Dynamics of Human and Rat Islet Amyloid Polypeptides.

Proteins·2026
Same journal

Stabilization of Bone Morphogenetic Protein-2 at Physiological pH: Contrasting Roles of CHAPS and Arginine in Aggregation Inhibition.

Proteins·2026
Same journal

Structural Insights Into the Function of Leishmania major Adenylosuccinate Lyase.

Proteins·2026
Same journal

Generalizing the Gaussian Network Model: Spanning-Tree Thermodynamics Shows Entropy-Driven KRAS Activation.

Proteins·2026
See all related articles

We developed HMMSTR-CM, a novel method for predicting protein contact maps. This approach combines fold recognition and ab initio techniques for accurate protein structure modeling, even without templates.

Area of Science:

  • Computational biology
  • Structural bioinformatics
  • Protein structure prediction

Background:

  • Accurate protein contact map prediction is crucial for understanding protein structure and function.
  • Existing methods face challenges in predicting complex protein topologies and folding pathways.

Purpose of the Study:

  • To introduce HMMSTR-CM, a novel computational method for enhanced protein contact map prediction.
  • To combine fold recognition and ab initio approaches for improved accuracy in protein structure modeling.

Main Methods:

  • Utilized HMMSTR (hidden Markov model for local sequence structure correlations) to calculate contact potentials.
  • Employed Bayesian methods for aligning target proteins against templates and generating contact maps.
  • Developed an ab initio method incorporating target contact potentials and a rule-based strategy for protein folding pathways.

Related Experiment Videos

  • Integrated fold recognition and ab initio methods for comprehensive contact map generation.

    • Main Results:

    • HMMSTR-CM successfully generated accurate, protein-like contact maps.
    • The combined approach demonstrated effectiveness even in cases lacking homologous templates.
    • Protein folding pathways were modeled, sometimes leading to unambiguous topology predictions.
    • Evaluated performance on CASP5 targets, showing promising results for the novel method.

    Conclusions:

    • HMMSTR-CM offers a robust and accurate method for protein contact map prediction.
    • The integration of fold recognition and ab initio strategies enhances prediction capabilities.
    • This method holds potential for advancing protein structure prediction and computational biology research.