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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
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 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: Jul 10, 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

CLEMAPS: multiple alignment of protein structures based on conformational letters.

Xin Liu1, Ya-Pu Zhao, Wei-Mou Zheng

  • 1Institute of Mechanics, Chinese Academy of Sciences, Beijing 100080, China.

Proteins
|November 6, 2007
PubMed
Summary

CLEMAPS is a novel tool for protein structure alignment using conformational letters to identify local similarities efficiently. It refines these findings with spatial consistency checks for accurate multiple structure alignments.

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Last Updated: Jul 10, 2026

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Area of Science:

  • Structural bioinformatics
  • Computational biology
  • Protein structure analysis

Background:

  • Multiple protein structure alignment is crucial for understanding protein function and evolution.
  • Existing algorithms face challenges in efficiently handling large datasets and complex structural variations.

Purpose of the Study:

  • To introduce CLEMAPS, a new computational tool for multiple protein structure alignment.
  • To leverage a novel approach using conformational letters for efficient detection of local structural similarities.

Main Methods:

  • Protein structures are converted into sequences of conformational letters representing discretized 3D segmental states.
  • A substitution matrix (CLESUM) quantifies similarity between conformational letters.
  • Center-star detection identifies fragments with local structural similarity.
  • Spatial consistency checks using atomic coordinates refine alignments, followed by core creation and polishing.

Main Results:

  • CLEMAPS efficiently detects local structural similarities using conformational letters and the CLESUM matrix.
  • The method successfully identifies consistent star duads and builds a core for multiple alignment.
  • The tool's utility is demonstrated across various protein structure ensembles.

Conclusions:

  • CLEMAPS offers an efficient and effective approach for multiple protein structure alignment.
  • The use of conformational letters and spatial consistency checks provides a robust framework for structural bioinformatics analysis.
  • This tool aids in the discovery of shared structural features across diverse protein families.