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Related Concept Videos

Protein Organization01:24

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 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 Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
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-protein Interfaces02:04

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...

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Related Experiment Video

Updated: Jun 23, 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

Testing the reliability of AI-generated protein structures.

Amanda Xu, Steven L Salzberg

    Biorxiv : the Preprint Server for Biology
    |June 22, 2026
    PubMed
    Summary
    This summary is machine-generated.

    AlphaFold2 and ColabFold have a low false positive rate in protein structure prediction. Unexpectedly, some high-scoring predictions revealed un-annotated pseudogenes in the human genome.

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

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    Last Updated: Jun 23, 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

    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

    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

    Area of Science:

    • Computational Biology
    • Genomics
    • Structural Biology

    Background:

    • Protein structure prediction tools like AlphaFold2 and ColabFold show high accuracy.
    • Understanding the limitations and potential false positive rates of these tools is crucial for reliable biological interpretation.

    Purpose of the Study:

    • To investigate the reliability and false positive rate of AlphaFold2 and ColabFold.
    • To assess the likelihood of these tools generating high-scoring structures for non-protein sequences.

    Main Methods:

    • Generated realistic but non-protein sequences.
    • Utilized ColabFold for structure prediction on these sequences.
    • Analyzed the frequency of high-scoring predictions for non-protein sequences.

    Main Results:

    • AlphaFold2 exhibits a small but non-zero false positive rate, estimated at approximately 1 in 435 using a pLDDT score threshold of 70.
    • Identified previously unknown and un-annotated pseudogenes in the human genome among high-scoring sequences.
    • These findings suggest potential inaccuracies in current human genome annotations regarding 5' untranslated regions of protein-coding genes.

    Conclusions:

    • AlphaFold2 and ColabFold are highly reliable, with a low false positive rate.
    • High-scoring predictions, even from non-coding regions, warrant further investigation for novel biological discoveries.
    • The study highlights the potential of structure prediction tools to uncover previously un-annotated genomic elements like pseudogenes.