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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 Organization01:13

Protein Organization

Overview
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 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...

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Related Experiment Video

Updated: Jun 19, 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

Evaluating protein similarity from coarse structures.

Yong Wang1, Ling-Yun Wu, Ji-Hong Zhang

  • 1Institute of Applied Mathematics, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, No. 55 Zhongguancun East Road, Beijing, 100080, China. ywang@amss.ac.cn

IEEE/ACM Transactions on Computational Biology and Bioinformatics
|October 31, 2009
PubMed
Summary

A new method represents protein structures using Feature Sequence of Surface (FSS) for efficient similarity assessment. This approach enables fast screening of large protein structure databases and offers a novel tool for quantitative analysis.

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Area of Science:

  • Structural bioinformatics
  • Computational biology
  • Biophysics

Background:

  • Understanding protein function requires assessing protein structure similarity.
  • Existing protein structure alignment methods are insufficient for rapid large-scale database screening.
  • Novel similarity measures are needed for efficient protein structure comparison.

Purpose of the Study:

  • To develop a novel representation for protein structures called Feature Sequence of Surface (FSS).
  • To create a new scoring scheme for measuring similarity between FSS representations.
  • To validate the proposed method's efficiency and effectiveness in protein structure analysis.

Main Methods:

  • Formulation of the Feature Sequence of Surface (FSS) representation for protein structures.
  • Development of a novel score scheme to quantify similarity between FSS representations.
  • Numerical experiments on four diverse protein datasets and classification of SARS coronavirus.

Main Results:

  • The proposed FSS method demonstrates simplicity, computational efficiency, and high speed.
  • Successful classification of SARS coronavirus using the new similarity measure.
  • Preliminary results show fast classification of the entire CATH v2.5.1 database.

Conclusions:

  • The FSS approach provides an efficient and fast method for protein structure similarity assessment.
  • This method offers a new quantitative tool for analyzing and comparing protein structures.
  • The approach is suitable for rapid screening and querying large-scale protein structure databases.