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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.

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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

STRALCP--structure alignment-based clustering of proteins.

Adam Zemla1, Brian Geisbrecht, Jason Smith

  • 1Computing Applications and Research, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA. adamz@llnl.gov

Nucleic Acids Research
|November 28, 2007
PubMed
Summary

Structure information alone can adequately classify proteins. Our STRALCP (STRucture ALignment-based Clustering of Proteins) algorithm identifies structurally conserved regions for effective protein clustering and classification.

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Last Updated: Jul 9, 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

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

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group
07:49

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Published on: August 16, 2017

Area of Science:

  • Bioinformatics
  • Structural Biology
  • Computational Biology

Background:

  • Protein structural annotation and classification are crucial for understanding protein function and interactions.
  • Analyzing sequence-structure correspondences aids in deciphering protein behavior.
  • Clustering protein domains by structural similarity is key for classification schemes.

Purpose of the Study:

  • To determine if structural information alone is sufficient for adequate protein structure classification.
  • To develop and present an algorithm for clustering protein structures based on structural similarity.

Main Methods:

  • Developed STRALCP (STRucture ALignment-based Clustering of Proteins) algorithm.
  • Identified global and local structural similarities between protein pairs.
  • Detected structurally conserved fragments (spans) within protein sets.
  • Utilized identified spans for automated protein structure clustering.

Main Results:

  • Demonstrated the effectiveness of structure information for protein classification.
  • Successfully clustered protein structures based on identified structurally conserved regions.
  • The STRALCP algorithm provides detailed similarity information.

Conclusions:

  • Protein structure information alone is sufficient for adequate classification.
  • The STRALCP algorithm offers a novel approach to protein clustering.
  • A web server is available for utilizing the STRALCP algorithm and its functionalities.