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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 Organization01:24

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 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 Folding01:22

Protein Folding

Overview

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Updated: Jun 21, 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

Alignment of multiple protein structures based on sequence and structure features.

M S Madhusudhan1, Benjamin M Webb, Marc A Marti-Renom

  • 1Department of Bioengineering and Therapeutic Sciences, University of California at San Francisco, San Francisco, CA 94158, USA.

Protein Engineering, Design & Selection : PEDS
|July 10, 2009
PubMed
Summary
This summary is machine-generated.

We developed SALIGN, a novel method for aligning multiple protein structures using sequence and structural features. SALIGN improves structural overlap and identifies more equivalent positions, aiding protein evolution and function studies.

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Last Updated: Jun 21, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction
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Published on: November 3, 2011

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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

Published on: July 16, 2017

Area of Science:

  • Structural Biology
  • Bioinformatics
  • Computational Biology

Background:

  • Comparing protein structures is essential for understanding protein evolution and function.
  • Accurate multiple protein structure alignment is a challenging but critical task in bioinformatics.

Purpose of the Study:

  • To introduce SALIGN, a new dynamic programming method for multiple protein structure alignment.
  • To benchmark SALIGN against existing methods and demonstrate its utility in comparative modeling.

Main Methods:

  • SALIGN optimizes a scoring function combining affine gap penalties with sequence and structure features (residue type, position, accessible surface area, secondary structure, local conformation).
  • Multiple alignments are constructed using a guide tree derived from pairwise alignment scores.
  • The method finds optimal alignments across a range of parameter values, reducing dependence on exact parameter settings.

Main Results:

  • SALIGN demonstrated a 15% improvement in structural overlap compared to HOMSTRAD and 14% over MUSTANG.
  • SALIGN identified more equivalent structural positions than TM-align (90% of cases) and CE (95% of cases).

Conclusions:

  • SALIGN provides a robust and accurate method for multiple protein structure alignment.
  • The improved accuracy of SALIGN facilitates applications such as comparative protein structure modeling.