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 Folding

Protein Folding

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

Proteome-wide analysis of protein stability in Escherichia coli under acid stress.

Journal of industrial microbiology & biotechnology·2026

Same author

Adoption of Standard Reference SNP Identifiers in Agricultural Genomics for Interoperability and Data Reuse.

Scientific data·2026

Same author

Delivering artificial intelligence-ready genomics with the Maize Genetics and Genomics Database.

Genetics·2026

Same author

GrainGenes: genetics, genomes, and pangenomes.

Genetics·2025

Same author

PET-FBA: A lightweight enzyme allocation and thermodynamics-constrained flux analysis approach to explore Escherichia coli metabolic adaptation to intracellular acidification.

Metabolic engineering·2025

Same author

Large Numbers of New Human Paralogs Discovered.

bioRxiv : the preprint server for biology·2025

Same journal

Tracking Synthetic Adhesins on Bacterial Surfaces with Immunofluorescence Microscopy.

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

Same journal

Post-Selection Methods for Analyzing mRNA Display Selections and Optimization of Hits.

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

Same journal

High-Performance Computing in Tandem Mass Spectrometry (MS/MS) Peptide Identification.

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

Same journal

Engineering and Adapting Disulfide-Containing Proteins to Enable Intracellular Functionality.

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

Same journal

AI-Driven Protein Research: From Prediction to Design.

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

Same journal

Methods for the In Vitro Selection of Protein and Peptide Libraries Using mRNA Display.

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

See all related articles

Search research articles

Related Experiment Video

Updated: Mar 13, 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

Predicting Protein Secondary Structure Using Consensus Data Mining (CDM) Based on Empirical Statistics and

Gaurav Kandoi^1,2, Sumudu P Leelananda³, Robert L Jernigan^1,4

¹Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA, USA.

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

|October 28, 2016

Summary

This summary is machine-generated.

Predicting protein secondary structure remains challenging. The Consensus Data Mining (CDM) method combines GOR V and Fragment Database Mining (FDM) for improved accuracy, especially when sequence fragments are unavailable.

Keywords:

Consensus data mining Fragment database mining GOR Machine learning Multiple sequence alignments Protein structure prediction Secondary structure

More Related Videos

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

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

Published on: July 14, 2015

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

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: Mar 13, 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

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

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

Published on: July 14, 2015

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

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:

Biochemistry
Bioinformatics
Computational Biology

Background:

Protein secondary structure prediction from amino acid sequences is a fundamental challenge in molecular biology.
Current prediction accuracies hover around 80%, necessitating improved methodologies.
Evolutionary information and machine learning approaches have significantly advanced prediction capabilities.

Purpose of the Study:

To review and present the Consensus Data Mining (CDM) technique for protein secondary structure prediction.
To detail the components of CDM: the GOR V algorithm and the Fragment Database Mining (FDM) approach.
To highlight CDM's hierarchical prediction strategy.

Main Methods:

The GOR V method utilizes a sliding window and generalized evolutionary information to predict secondary structural elements.
Fragment Database Mining (FDM) leverages experimentally determined structural fragments identified through sequence similarity.
The Consensus Data Mining (CDM) method integrates GOR V and FDM predictions hierarchically.

Main Results:

CDM provides consensus predictions by combining outputs from GOR V and FDM.
When sequence fragments are unavailable, CDM defaults to GOR V for prediction.
The integrated approach aims to enhance the accuracy of protein secondary structure prediction.

Conclusions:

The CDM technique offers a robust approach to protein secondary structure prediction by combining empirical and data-driven methods.
CDM's hierarchical strategy ensures prediction capability even with limited sequence fragment data.
An online server for CDM is available for public use at http://gor.bb.iastate.edu/cdm/.