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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 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
Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
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 Complex Assembly02:41

Protein Complex Assembly

Proteins can form homomeric complexes with another unit of the same protein or heteromeric complexes with different types.  Most protein complexes self-assemble spontaneously via ordered pathways, while some proteins need assembly factors that guide their proper assembly. Despite the crowded intracellular environment, proteins usually interact with their correct partners and form functional complexes.
Many viruses self-assemble into a fully functional unit using the infected host cell to...

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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

Implementation of a parallel protein structure alignment service on cloud.

Che-Lun Hung1, Yaw-Ling Lin

  • 1Department of Computer Science and Communication Engineering, Providence University, 200, Sec. 7, Taiwan Boulevard, Shalu Dist., Taichung 43301, Taiwan.

International Journal of Genomics
|May 15, 2013
PubMed
Summary
This summary is machine-generated.

We developed a parallel protein structure alignment service using Hadoop. This service accurately refines protein alignments and offers scalable computational performance for large datasets.

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Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

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Last Updated: May 11, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction
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Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
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Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

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

Published on: July 16, 2017

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Structural Biology

Background:

  • Protein structure alignment is crucial for identifying evolutionary relationships.
  • Existing online tools for protein structure comparison are limited.
  • Large-scale analysis of protein structures requires efficient computational methods.

Purpose of the Study:

  • To propose a parallel protein structure alignment service using the Hadoop framework.
  • To enhance the accuracy of protein structure alignments through a refinement algorithm.
  • To improve the computational performance for processing vast numbers of protein structures.

Main Methods:

  • Implementation of a protein structure alignment algorithm using MapReduce.
  • Development of a refinement algorithm to improve alignment accuracy.
  • Utilizing the Hadoop distributed framework for parallel processing.

Main Results:

  • The proposed algorithm refines protein structure alignments more accurately than existing methods.
  • Experimental results using PDB data confirm improved alignment accuracy.
  • Computational performance scales proportionally with the number of processors.

Conclusions:

  • The parallel protein structure alignment service provides accurate and efficient analysis.
  • Hadoop-based MapReduce enables scalable processing of large protein structure datasets.
  • This approach advances the study of evolutionary relationships through enhanced structural bioinformatics tools.