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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...
Conservation of Protein Domains02:26

Conservation of Protein Domains

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...
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...
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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Related Experiment Video

Updated: May 11, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

DALIX: optimal DALI protein structure alignment.

Inken Wohlers1, Rumen Andonov, Gunnar W Klau

  • 1Genominformatik, Universität Duisburg-Essen/Universitätsklinikum, Germany. inken.wohlers@uni-due.de

IEEE/ACM Transactions on Computational Biology and Bioinformatics
|May 25, 2013
PubMed
Summary
This summary is machine-generated.

We developed DALIX, an exact algorithm for optimal protein structure alignment using the DALI scoring model. This method precisely evaluates the popular DALI heuristic, finding optimal alignments and identifying its limitations for small proteins.

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A Protocol for Computer-Based Protein Structure and Function Prediction
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A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Related Experiment Videos

Last Updated: May 11, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

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

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

Area of Science:

  • Computational Biology
  • Structural Bioinformatics
  • Algorithm Development

Background:

  • Protein structure alignment is crucial for understanding protein function and evolution.
  • The DALI software tool is a widely used heuristic for protein structure alignment based on interresidue distance matrices.
  • Existing methods often struggle with optimality guarantees and computational efficiency.

Purpose of the Study:

  • To develop a mathematical model and exact algorithm for optimal protein structure alignment using the DALI scoring model.
  • To introduce a novel integer linear programming approach for distance matrix comparison.
  • To provide a framework for evaluating the accuracy of heuristic alignment methods like DALI.

Main Methods:

  • Formulated an integer linear programming model for protein structure alignment based on the DALI scoring system.
  • Introduced a novel constraint handling negative scores via Lagrangian relaxation.
  • Developed the DALIX algorithm, applicable to various distance matrix-based scoring schemes.
  • Optimized the consideration of interresidue distance pairs to manage computational complexity.

Main Results:

  • Computed provably score-optimal DALI alignments for diverse protein datasets.
  • Enabled the first rigorous mathematical evaluation of the DALI heuristic's performance.
  • Demonstrated that DALI generally produces optimal or near-optimal alignments.
  • Identified a specific subset of small proteins where DALI fails to find significant alignments despite their existence.

Conclusions:

  • The DALIX algorithm offers a precise method for protein structure alignment and evaluation.
  • The DALI heuristic is largely accurate but has limitations, particularly for small protein structures.
  • This work provides a benchmark for assessing and improving protein structure alignment algorithms.