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 Concept Videos

Design Example: Measuring Distance Between Two Points with Obstructions01:10

Design Example: Measuring Distance Between Two Points with Obstructions

When measuring distances in areas with physical obstructions, such as a lake in a field, surveyors must employ techniques to calculate accurate lengths without direct line measurements. One effective method is the offset technique, which allows for precise distance estimation over inaccessible stretches.In this scenario, a surveyor must measure a side of an area that crosses a lake. Since the measuring tape cannot span the lake, the surveyor begins by establishing a baseline that aligns with...
Structural Classification of Joints01:20

Structural Classification of Joints

Joints, also known as articulations, are classified based on their structural characteristics, i.e., based on whether the articulating surfaces of the adjacent bones are directly connected by fibrous connective tissue or cartilage, or whether the articulating surfaces contact each other within a fluid-filled joint cavity. These differences serve to divide the joints of the body into three structural classifications.
A fibrous joint is where the adjacent bones are united by fibrous connective...
Deformation of Member under Multiple Loadings01:11

Deformation of Member under Multiple Loadings

When a rod is made of different materials or has various cross-sections, it must be divided into parts that meet the necessary conditions for determining the deformation. These parts are each characterized by their internal force, cross-sectional area, length, and modulus of elasticity. These parameters are then used to compute the deformation of the entire rod.
In the case of a member with a variable cross-section, the strain is not constant but depends on the position. The deformation of an...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Altering under-represented DNA sequences elevates bacterial transformation efficiency.

mBio·2023
Same author

Fallacy of the Unique Genome: Sequence Diversity within Single <i>Helicobacter pylori</i> Strains.

mBio·2017
Same author

Analysis of nanopore data using hidden Markov models.

Bioinformatics (Oxford, England)·2015
Same author

Error rates for nanopore discrimination among cytosine, methylcytosine, and hydroxymethylcytosine along individual DNA strands.

Proceedings of the National Academy of Sciences of the United States of America·2013
Same author

Complete genome sequence of Pyrobaculum oguniense.

Standards in genomic sciences·2013
Same author

Automated forward and reverse ratcheting of DNA in a nanopore at 5-Ã… precision.

Nature biotechnology·2012
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

Related Experiment Video

Updated: Jun 28, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Model quality assessment using distance constraints from alignments.

Martin Paluszewski1, Kevin Karplus

  • 1Department of Computer Science, University of Copenhagen, Copenhagen, Denmark.

Proteins
|November 13, 2008
PubMed
Summary
This summary is machine-generated.

This study introduces a new protein model quality assessment (MQA) method using distance constraints from template alignments. The Undertaker program achieves results comparable to top MQA methods and proposes Kendall's tau for better evaluation.

More Related Videos

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

Related Experiment Videos

Last Updated: Jun 28, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

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

Area of Science:

  • Computational Biology
  • Structural Bioinformatics
  • Protein Structure Prediction

Background:

  • Model quality assessment (MQA) is crucial for selecting accurate protein structures from computational predictions.
  • Existing MQA methods often rely on limited scoring metrics, necessitating improved approaches.
  • Accurate MQA guides the selection of protein models that best represent the true 3D structure.

Purpose of the Study:

  • To develop and implement a novel approach for protein model quality assessment (MQA).
  • To introduce a new evaluation metric, Kendall's tau, for assessing MQA performance.
  • To improve the accuracy and interpretability of scores assigned to protein structure models.

Main Methods:

  • Developed a new MQA approach based on distance constraints (both contact and noncontact) extracted from template-sequence alignments.
  • Implemented the method in the Undertaker program for protein structure prediction.
  • Compared the performance against existing MQA methods using CASP7 targets and introduced Kendall's tau for evaluation.

Main Results:

  • The Undertaker program's MQA method demonstrated performance comparable to the best methods assessed in CASP7.
  • The proposed Kendall's tau evaluation measure showed higher interpretability and better agreement with intuitive assessments of MQA quality.
  • Extracted noncontact constraints alongside contact constraints provide novel information for MQA.

Conclusions:

  • The novel MQA approach based on distance constraints is effective and competitive with current state-of-the-art methods.
  • Kendall's tau is proposed as a more intuitive and reliable metric for evaluating MQA performance in future assessments.
  • The Undertaker program offers a valuable tool for protein structure prediction and quality assessment.