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

Structure-dependent sequence alignment for remotely related proteins.

An-Suei Yang1

  • 1Department of Pharmacology and Columbia Genome Center, Columbia University, 630 West 168th street, PH 7 W Room 318, New York, NY 10032, USA. ay1@columbia.edu

Bioinformatics (Oxford, England)
|December 20, 2002
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

Correction to "Functionalized Terpolymer-Brush-Based Biointerface with Improved Antifouling Properties for Ultra-Sensitive Direct Detection of Virus in Crude Clinical Samples".

ACS applied materials & interfaces·2025
Same author

Performance evaluation of predictive models for detecting MMR gene mutations associated with Lynch syndrome in cancer patients in a Chinese cohort in Taiwan.

International journal of cancer·2024
Same author

Mismatch Repair (MMR) Gene Mutation Carriers Have Favorable Outcome in Colorectal and Endometrial Cancer: A Prospective Cohort Study.

Cancers·2024
Same author

Negligible risk of surface transmission of SARS-CoV-2 in public transportation.

Journal of travel medicine·2023
Same author

Computational Analysis of Antibody Paratopes for Antibody Sequences in Antibody Libraries.

Methods in molecular biology (Clifton, N.J.)·2022
Same author

Antibody CDR amino acids underlying the functionality of antibody repertoires in recognizing diverse protein antigens.

Scientific reports·2022
Same journal

3DICE: Interpretable 3D Cross-Modal Learning for Drug-Target Interaction Prediction and Large-Scale Drug Discovery.

Bioinformatics (Oxford, England)·2026
Same journal

KASSPer: Kinase Active Site Structure Prediction using Protein and Ligand Language Models and Its Application to Virtual Screening.

Bioinformatics (Oxford, England)·2026
Same journal

IDR searcher: a search engine solution for public image resources.

Bioinformatics (Oxford, England)·2026
Same journal

KCFtools: Rapid alignment-free method for introgression screening and GWAS using k-mer profiles.

Bioinformatics (Oxford, England)·2026
Same journal

Meta2DB: Curated shotgun metagenomic feature sets and metadata for health state prediction.

Bioinformatics (Oxford, England)·2026
Same journal

conMItion: an R package adjusting confounding factors for associations in multi-omics.

Bioinformatics (Oxford, England)·2026
See all related articles

Improving protein structure prediction requires accurate sequence-template alignment. A new method integrating sequence and structural information enhances alignment accuracy for distantly related protein pairs, increasing correctly aligned residues by 27%.

Area of Science:

  • Computational Biology
  • Structural Bioinformatics
  • Protein Modeling

Background:

  • Comparative modeling accuracy relies on sequence-template alignment.
  • Traditional methods struggle with distantly related protein pairs.
  • Integrating structural information can improve alignment accuracy.

Purpose of the Study:

  • To develop a sequence-template alignment method using both sequence and structural information.
  • To enhance the accuracy of alignments for distantly related protein pairs.

Main Methods:

  • Developed a structure-dependent sequence alignment (SDSA) procedure.
  • Optimized SDSA on a training set of 412 protein pairs with low sequence identity (8%) but similar structures.
  • Applied SDSA to extend PSI-BLAST local alignments, creating composite global alignments.

Related Experiment Videos

Main Results:

  • The composite alignment procedure was tested on 1421 protein pairs with marginal sequence similarity (13%).
  • Achieved an average of 27% increase in correctly aligned residues compared to standard PSI-BLAST.
  • Demonstrated improved accuracy in sequence-template alignment for challenging protein pairs.

Conclusions:

  • The integrated sequence-structure alignment method significantly improves alignment accuracy.
  • This approach enhances protein structure prediction for distantly related proteins.
  • The SDSA procedure offers a valuable tool for structural bioinformatics.