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

Protein Folding01:22

Protein Folding

Overview
Protein Folding01:25

Protein Folding

Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...
Protein Folding01:22

Protein Folding

Overview
Protein and Protein Structure02:15

Protein and Protein Structure

Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme can...
Protein Folding Quality Check in the RER01:29

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...
Protein and Protein Structures02:15

Protein and Protein Structures

Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme can...

You might also read

Related Articles

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

Sort by
Same author

Stable dry reforming of methane over Ni-Pt bimetallic catalysts supported on KIT-5 in a continuous flow system.

RSC advances·2026
Same author

Effect of Si/Zr ratio on the catalytic behavior of Pt-Cu/Zr-SBA-15 in continuous methane dry reforming.

RSC advances·2026
Same author

Hydrogen in transport: a review of opportunities, challenges, and sustainability concerns.

RSC advances·2025
Same author

Dissociation and radiative stabilization of the indene cation: The nature of the C-H bond and astrochemical implications.

The Journal of chemical physics·2025
Same author

High-throughput proteomic analysis of candidate biomarker changes in gingival crevicular fluid after treatment of chronic periodontitis.

Journal of periodontal research·2018
Same author

In-Situ Growth of CoS Nanoparticles Onto Electrospun Graphitized Carbon Nanofibers as an Efficient Counter Electrode for Dye-Sensitized Solar Cells.

Journal of nanoscience and nanotechnology·2018

Related Experiment Video

Updated: May 17, 2026

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

ASTRO-FOLD 2.0: an Enhanced Framework for Protein Structure Prediction.

A Subramani1, Y Wei, C A Floudas

  • 1Dept. of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544.

Aiche Journal. American Institute of Chemical Engineers
|October 11, 2012
PubMed
Summary
This summary is machine-generated.

ASTRO-FOLD 2.0 accurately predicts protein 3-D structures using novel optimization methods. This computational approach enhances protein structure prediction accuracy for biological research.

More Related Videos

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

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
05:08

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

Related Experiment Videos

Last Updated: May 17, 2026

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

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

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
05:08

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

Area of Science:

  • Computational Biology
  • Structural Bioinformatics
  • Protein Structure Prediction

Background:

  • Accurate three-dimensional (3-D) protein structure prediction from amino acid sequences is crucial for understanding protein function.
  • Existing methods often face challenges in achieving high accuracy, necessitating the development of novel computational approaches.

Purpose of the Study:

  • To present ASTRO-FOLD 2.0, a first principles-based computational method for predicting protein 3-D structures.
  • To detail the key novel features and optimization techniques integrated into the ASTRO-FOLD 2.0 pipeline.

Main Methods:

  • Secondary structure prediction via an optimization-based consensus approach.
  • β-sheet topology and residue-to-residue contact prediction using mixed-integer linear optimization (MILP).
  • Loop residue structure refinement using dihedral angle clustering and non-linear optimization (NLP).
  • 3-D structure generation employing deterministic global optimization and stochastic conformational space annealing with the ECEPP/3 potential.
  • Near-native structure selection using the ICON clustering approach.
  • Enhanced bound generation utilizing chemical shift data from SPARTA and CS23D.

Main Results:

  • ASTRO-FOLD 2.0 was evaluated on 47 blind targets from the CASP9 experiment.
  • The study presents computational results demonstrating the performance of the integrated prediction pipeline.

Conclusions:

  • ASTRO-FOLD 2.0 represents a significant advancement in computational protein structure prediction.
  • The combination of novel optimization techniques and advanced algorithms improves the accuracy of predicted protein structures.