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

Conserved Binding Sites

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...

Protein Organization

Protein Organization

Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence....

Protein Organization

Protein Organization

Protein and Protein Structure

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...

Protein Folding

Protein Folding

Protein Folding

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...

You might also read

Related Articles

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

Sort by

Same author

MAMMAL - Molecular Aligned Multi-Modal Architecture and Language for biomedical discovery.

npj drug discovery·2026

Same author

hexABC seeking the physical code of DNA.

Nature communications·2026

Same author

Engineering Endogenous T Cell Receptors to Recognize Cancer Neoantigens Using a Hybrid Physics-AI Approach.

bioRxiv : the preprint server for biology·2026

Same author

Nonequilibrium Theory for Molecular Machine Design.

ArXiv·2026

Same author

Seeking Biology's Physics Stories: Simplify, Simplify.

Annual review of biophysics·2026

Same author

The NMR Exchange Format (NEF): Specification and Applications.

bioRxiv : the preprint server for biology·2026

Search research articles

Related Experiment Video

Updated: Mar 12, 2026

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

Blind protein structure prediction using accelerated free-energy simulations.

Alberto Perez¹, Joseph A Morrone¹, Emiliano Brini¹

¹Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA.

Science Advances

|November 17, 2016

Summary

A new method called Modeling Employing Limited Data (MELD) can now accurately and quickly predict protein structures using molecular dynamics simulations. This breakthrough enables reliable protein structure prediction in scientific research and competitions.

Keywords:

Protein folding molecular dynamics replica exchange simulations structure prediction

More Related Videos

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

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

Published on: July 25, 2013

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

Related Experiment Videos

Last Updated: Mar 12, 2026

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

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

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

Published on: July 25, 2013

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

Area of Science:

Computational biology
Structural biology
Biophysics

Background:

Predicting protein structures is crucial for understanding biological functions.
Molecular dynamics simulations are powerful but computationally intensive.
New acceleration methods are needed to make simulations feasible for complex problems.

Purpose of the Study:

To introduce and validate a novel acceleration method for protein structure prediction.
To demonstrate the feasibility of using this method in a competitive setting.

Main Methods:

Modeling Employing Limited Data (MELD) is a new acceleration technique for molecular dynamics simulations.
The method was tested within the Critical Assessment of Structure Prediction (CASP) blind competition.

Main Results:

MELD proved to be a key proof of principle for accelerated protein structure prediction.
The method demonstrated sufficient speed and accuracy for predicting native protein structures.

Conclusions:

Boltzmann-satisfying techniques, like MELD, are now viable for accurate protein structure prediction.
This advancement has significant implications for structural biology and drug discovery.