Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Molecular Models

Molecular Models

Physical models representing molecular architectures of chemical compounds play essential roles in understanding chemistry. The use of molecular models makes it easier to visualize the structures and shapes of atoms and molecules.

Mechanistic Models: Compartment Models in Algorithms for Numerical Problem Solving

Mechanistic Models: Compartment Models in Algorithms for Numerical Problem Solving

Mechanistic models play a crucial role in algorithms for numerical problem-solving, particularly in nonlinear mixed effects modeling (NMEM). These models aim to minimize specific objective functions by evaluating various parameter estimates, leading to the development of systematic algorithms. In some cases, linearization techniques approximate the model using linear equations.
In individual population analyses, different algorithms are employed, such as Cauchy's method, which uses a...

Protein Folding Quality Check in the RER

Protein Folding Quality Check in the RER

ER is the primary site for the maturation and folding of soluble and transmembrane secretory proteins. The calnexin cycle is a specific chaperone system that folds and assesses the confirmation of N-glycosylated proteins before they can exit the ER lumen. The primary players of this quality check pipeline are the lectins, ER-resident chaperones, and a glucosyl transferase enzyme. In case the calnexin system in the lumen fails to salvage a misfolded protein, it is transported to the cytoplasm...

You might also read

Related Articles

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

Sort by

Same author

Pathogenesis of Noonan Syndrome is Modulated by NOC2L, a Novel Interactor of LZTR1 Leading to Impaired P53 Signalling.

The Journal of clinical endocrinology and metabolism·2025

Same author

Highlights of Model Quality Assessment in CASP16.

Proteins·2025

Same author

Prediction and quality assessment of protein quaternary structure models using the MultiFOLD2 and ModFOLDdock2 servers.

Nucleic acids research·2025

Same author

Inter-platelet communication driving thrombus formation is regulated by extracellular calpain-1 cleavage of connexin 62.

Haematologica·2025

Same author

Beyond AlphaFold2: The Impact of AI for the Further Improvement of Protein Structure Prediction.

Methods in molecular biology (Clifton, N.J.)·2024

Same author

QSOX2 Deficiency-induced short stature, gastrointestinal dysmotility and immune dysfunction.

Nature communications·2024

Same journal

Mapping the 3D Chromosome Organization of a Biosynthetic Gene Cluster by Capture Hi-C (CHi-C).

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

Mapping the 3D Chromosome Organization of Streptomyces by Hi-C.

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

CUT&Tag Epigenomic Profiling of Biosynthetic Gene Clusters in Arabidopsis thaliana.

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

Rhizobium rhizogenes-Mediated Hairy Root Transformation Protocol for Lotus japonicus and Other Legumes.

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

Characterization of Bioactive Saponins from Sea Cucumbers.

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

Methods for Functional Validation of Terpenoid Metabolic Clusters in Nicotiana benthamiana and Aspergillus oryzae.

Methods in molecular biology (Clifton, N.J.)·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Aug 5, 2025

Author Spotlight: Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps

Author Spotlight: Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps

Published on: July 19, 2024

Using Local Protein Model Quality Estimates to Guide a Molecular Dynamics-Based Refinement Strategy.

Recep Adiyaman¹, Liam J McGuffin²

¹School of Biological Sciences, University of Reading, Reading, UK.

Methods in Molecular Biology (Clifton, N.J.)

|March 24, 2023

Summary

This summary is machine-generated.

This study introduces a new method to improve 3D protein models by using local quality scores to guide molecular dynamics (MD) refinement. This approach enhances accuracy and consistency in predicted protein structures.

Keywords:

Critical Assessment of Techniques for Protein Structure Prediction (CASP)Model quality assessment (MQA)Molecular dynamics Protein model refinement Protein modelling Protein structure prediction Tertiary structure prediction

More Related Videos

A Protocol for Computer-Based Protein Structure and Function Prediction

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Stability and Structure of Bat Major Histocompatibility Complex Class I with Heterologous β2-Microglobulin

Stability and Structure of Bat Major Histocompatibility Complex Class I with Heterologous β2-Microglobulin

Published on: March 10, 2021

Related Experiment Videos

Last Updated: Aug 5, 2025

Author Spotlight: Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps

Author Spotlight: Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps

Published on: July 19, 2024

A Protocol for Computer-Based Protein Structure and Function Prediction

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Stability and Structure of Bat Major Histocompatibility Complex Class I with Heterologous β2-Microglobulin

Stability and Structure of Bat Major Histocompatibility Complex Class I with Heterologous β2-Microglobulin

Published on: March 10, 2021

Area of Science:

Computational biology
Structural bioinformatics
Protein structure prediction

Background:

Protein 3D model refinement aims to correct errors and improve accuracy.
Molecular dynamics (MD) simulations with restraints are effective refinement methods.
Previous methods like ReFOLD lacked reliable guidance for consistent quality improvement, especially for template-based modeling.

Purpose of the Study:

To enhance the accuracy of predicted 3D protein models.
To address limitations in existing MD-based refinement protocols.
To introduce a novel guidance mechanism for protein model refinement.

Main Methods:

Utilizing local quality assessment scores from ModFOLD6 to guide MD-based refinement.
Comparing a new local quality assessment-guided MD protocol against the original ReFOLD method.
Evaluating performance using various official scoring methods and per-residue accuracy.

Main Results:

The local quality assessment-guided MD protocol demonstrates consistent improvements in predicted 3D model quality.
Guiding refinement with per-residue accuracy scores prevents undesired structural deviations.
The new protocol shows improved performance over the original ReFOLD method.

Conclusions:

Local quality assessment scores provide a reliable mechanism for guiding MD-based protein model refinement.
The proposed method leads to more accurate and structurally consistent 3D protein models.
This approach offers a significant advancement in protein structure prediction refinement.