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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.
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...
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
Protein and Protein Structures02:15

Protein and Protein Structures

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...

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Updated: May 22, 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

CSA: comprehensive comparison of pairwise protein structure alignments.

Inken Wohlers1, Noël Malod-Dognin, Rumen Andonov

  • 1Life Sciences Group, Centrum Wiskunde & Informatica, Science Park 123, 1098 XG Amsterdam, The Netherlands. I.Wohlers@cwi.nl

Nucleic Acids Research
|May 4, 2012
PubMed
Summary

The CSA web server offers advanced protein structure alignment computation and comparison. It provides valuable insights into structural relationships and similarities between protein pairs.

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Area of Science:

  • Bioinformatics
  • Structural Biology
  • Computational Biology

Background:

  • Protein structure alignment is crucial for understanding evolutionary relationships and functional similarities.
  • Existing tools may lack comprehensive comparison features or efficient alignment algorithms.

Purpose of the Study:

  • To develop and present CSA, a web server for robust protein structure alignment analysis.
  • To provide a platform for computing, evaluating, and comparing pairwise protein structure alignments.

Main Methods:

  • Utilizes an exact alignment engine for optimal and heuristic alignments.
  • Employs inter-residue distance-based scoring methods including contact map overlap, PAUL, DALI, and MATRAS.
  • Integrates multiple quality measures and visualizations for alignment comparison.

Main Results:

  • CSA computes high-quality protein structure alignments.
  • The server facilitates comprehensive evaluation and comparison of diverse alignment types.
  • Intuitive visualizations aid in interpreting structural relationships.

Conclusions:

  • CSA is a valuable tool for researchers studying protein structural similarities.
  • The web server enhances insights into the structural relationships of protein pairs.
  • CSA supports the advancement of structural bioinformatics research.