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Related Concept Videos

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...
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...
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 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 Organization01:13

Protein Organization

Overview
Protein Organization01:13

Protein Organization

Overview

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Related Experiment Video

Updated: Jun 28, 2026

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

[Trial to predict interactions between proteins and biomolecules based on their three-dimensional structures].

Kei Yura1

  • 1Graduate School of Humanities and Sciences, Ochanomizu University, Tokyo, Japan. yura.kei@ocha.ac.jp

Yakugaku Zasshi : Journal of the Pharmaceutical Society of Japan
|November 5, 2008
PubMed
Summary

Scientists are developing new methods to predict protein functions from 3D structures, aiding in understanding complex molecular mechanisms and utilizing vast genomic data.

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Related Experiment Videos

Last Updated: Jun 28, 2026

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

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

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

Published on: July 16, 2017

Area of Science:

  • Structural biology
  • Genomics
  • Bioinformatics

Context:

  • Massive datasets from genome sequencing and omics projects offer insights into cellular activity.
  • Challenges exist in fully utilizing the generated DNA sequence, protein 3D structure, and RNA expression data.
  • Protein 3D structure prediction is advancing, creating a demand for functional prediction methods.

Purpose:

  • To present observations on the growth of protein 3D structure data.
  • To describe the development of methods for predicting protein functions from 3D structures.
  • To demonstrate the accuracy of these methods in identifying RNA and ligand interfaces.

Summary:

  • A high proportion of protein 3D structures from genome sequences are now predictable.
  • Developed methods accurately predict RNA and ligand interfaces using 3D structures and DNA sequences.
  • These predictions aid in deducing the atomic structures of molecular complexes.

Impact:

  • Enables more effective utilization of large-scale biological data.
  • Facilitates a deeper understanding of molecular mechanisms and cellular functions.
  • Supports the accurate determination of complex atomic structures through computational prediction.