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 Video

Updated: Jun 28, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

Defining and computing optimum RMSD for gapped and weighted multiple-structure alignment.

Xueyi Wang1, Jack Snoeyink

  • 1Department of Mathematics and Computer Science, Northwest Nazarene University, 623 Holly St., Nampa, ID 83686-5897, USA. xwang@nnu.edu

IEEE/ACM Transactions on Computational Biology and Bioinformatics
|November 8, 2008
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

The relationship between anxiety and patent foramen ovale: a preliminary study.

BMC psychology·2026
Same author

Triple-modality management of complex septated chronic subdural hematoma: a preliminary technical note on feasibility and safety.

Frontiers in neurology·2026
Same author

Prognosis of renal re-transplantation for chronic graft failure.

Frontiers in surgery·2026
Same author

Dissociation between subjective sleep quality and lipid dysregulation in underground miners: night shift work as an independent risk factor for hypercholesterolemia.

Frontiers in public health·2026
Same author

Transplantation of active mitochondria condensed in liquid-liquid phase-separated hydrogels ameliorates myocardial ischemia-reperfusion injury.

Nature communications·2026
Same author

Cardiac reprogramming via transient overexpression of P-glycoprotein alleviates doxorubicin-induced cardiotoxicity in mice and pigs.

Nature communications·2026
Same journal

circ2DGNN: circRNA-Disease Association Prediction via Transformer-Based Graph Neural Network.

IEEE/ACM transactions on computational biology and bioinformatics·2024
Same journal

Hierarchical Hypergraph Learning in Association- Weighted Heterogeneous Network for miRNA- Disease Association Identification.

IEEE/ACM transactions on computational biology and bioinformatics·2024
Same journal

Discriminative Domain Adaption Network for Simultaneously Removing Batch Effects and Annotating Cell Types in Single-Cell RNA-Seq.

IEEE/ACM transactions on computational biology and bioinformatics·2024
Same journal

MLW-BFECF: A Multi-Weighted Dynamic Cascade Forest Based on Bilinear Feature Extraction for Predicting the Stage of Kidney Renal Clear Cell Carcinoma on Multi-Modal Gene Data.

IEEE/ACM transactions on computational biology and bioinformatics·2024
Same journal

An End-to-End Knowledge Graph Fused Graph Neural Network for Accurate Protein-Protein Interactions Prediction.

IEEE/ACM transactions on computational biology and bioinformatics·2024
Same journal

Generative Biomedical Event Extraction With Constrained Decoding Strategy.

IEEE/ACM transactions on computational biology and bioinformatics·2024
See all related articles

This study introduces weighted Root Mean Square Deviation (RMSD) for multiple structure alignment, establishing the average structure as a consensus. A novel algorithm efficiently finds optimal alignments and identifies conserved regions by down-weighting outliers.

Area of Science:

  • Computational Biology
  • Structural Bioinformatics
  • Biophysics

Background:

  • Pairwise structure alignment commonly uses Root Mean Square Deviation (RMSD) to quantify structural similarity.
  • Existing RMSD optimization methods are well-established for pairwise comparisons.

Purpose of the Study:

  • To extend Root Mean Square Deviation (RMSD) to a weighted version for aligning multiple protein structures.
  • To develop an efficient algorithm for optimizing weighted RMSD and identifying conserved structural regions.

Main Methods:

  • Extension of Root Mean Square Deviation (RMSD) to weighted RMSD for multiple structures using multiplicative weights.
  • Development of a near-linear iterative algorithm to converge weighted RMSD to a local minimum.
  • Proposal of a heuristic method for outlier removal using B-factors and positional deviations as weights.

More Related Videos

Structure and Coordination Determination of Peptide-metal Complexes Using 1D and 2D 1H NMR
14:44

Structure and Coordination Determination of Peptide-metal Complexes Using 1D and 2D 1H NMR

Published on: December 16, 2013

Related Experiment Videos

Last Updated: Jun 28, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

Structure and Coordination Determination of Peptide-metal Complexes Using 1D and 2D 1H NMR
14:44

Structure and Coordination Determination of Peptide-metal Complexes Using 1D and 2D 1H NMR

Published on: December 16, 2013

Main Results:

  • Demonstration that weighted RMSD for all pairs equals weighted RMSD to the average structure, implying the average is a consensus.
  • Rapid convergence of the developed algorithm to a local minimum across 10,000 gapped alignment experiments on protein families.
  • Successful identification of well-aligned positions representing the structural conserved region through iterative weighting.

Conclusions:

  • Weighted RMSD provides a robust measure for multiple structure alignment, with the average structure serving as a reliable consensus.
  • The developed iterative algorithm efficiently optimizes weighted RMSD and is effective in identifying conserved structural elements.
  • The heuristic outlier removal method enhances the accuracy of structural conserved region identification in protein families.