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

Multiple mapping method: a novel approach to the sequence-to-structure alignment problem in comparative protein

Brajesh K Rai1, András Fiser

  • 1Department of Biochemistry and Seaver Center for Bioinformatics, Albert Einstein College of Medicine, Bronx, New York 10461, USA.

Proteins
|January 27, 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

XL-MS-Guided Structure Prediction of Disordered <i>Encephalitozoon hellem</i> Proteins.

bioRxiv : the preprint server for biology·2026
Same author

Conservation of Human IgSF Proteins Throughout Eukaryotic Evolution.

Genome biology and evolution·2026
Same author

Overcoming research bias: The untapped potential of biomedically important but understudied proteins.

iScience·2025
Same author

Inhibition of HDAC7 reprograms the histone H3.3 landscape to induce heterochromatin spreading and DNA replication defects in cancer cells.

The Journal of biological chemistry·2025
Same author

Optimization of a sarbecovirus llama nanobody-antigen binding interface via a combined computational and phage display protein engineering approach.

Proceedings of the National Academy of Sciences of the United States of America·2025
Same author

GliaTrap is a biodegradable, non-swelling and non-inflammatory hydrogel with tuned release of CXCL12 to attract migrating glioblastoma cells.

Scientific reports·2025
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

A new Multiple Mapping Method (MMM) improves protein structure modeling by combining alternative sequence alignments. This approach significantly reduces alignment errors, enhancing accuracy in comparative modeling.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Structural Biology

Background:

  • Comparative protein structure modeling relies heavily on accurate sequence alignments.
  • Existing alignment methods have limitations, often producing suboptimal results for specific regions.
  • Combining diverse alignment strategies is crucial for improving overall accuracy.

Purpose of the Study:

  • To develop a novel algorithm, the Multiple Mapping Method (MMM), for generating improved protein sequence alignments.
  • To address the challenge of inconsistent performance across different alignment techniques.
  • To enhance the accuracy of comparative protein structure modeling.

Main Methods:

  • The Multiple Mapping Method (MMM) algorithm identifies alternatively aligned regions from multiple input alignments.

Related Experiment Videos

  • A composite scoring function evaluates the suitability of these alternative segments within the template's structural context.
  • Optimal segments are merged with core alignment regions to produce the final MMM alignment.

    • Main Results:

    • MMM demonstrated statistically significant improvements in alignment accuracy across 11 tested combinations of alignment methods.
    • Alignment errors were reduced by 3% to 17% in tests involving 1400 protein pairs.
    • MMM outperformed two existing alignment meta-servers and is computationally efficient.

    Conclusions:

    • The Multiple Mapping Method (MMM) offers a robust solution for improving protein sequence alignments in comparative modeling.
    • Its ability to integrate diverse alignment strategies leads to enhanced accuracy and reliability.
    • MMM's computational efficiency makes it suitable for large-scale genomic studies and protein modeling applications.