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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.
Proteomics01:33

Proteomics

A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term proteomics...
Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Protein-protein Interfaces02:04

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...
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...
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...

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Related Experiment Video

Updated: Jun 6, 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

A data-mining approach for multiple structural alignment of proteins.

Wing-Yan Siu1, Nikos Mamoulis, Siu-Ming Yiu

  • 1Department of Computer Science, the University of Hong Kong, Pokfulam Road, Hong Kong, China.

Bioinformation
|November 17, 2010
PubMed
Summary
This summary is machine-generated.

This study introduces a novel data-mining approach for protein structural alignment, identifying conserved substructures without sequence order. The method efficiently finds alignments in protein interfaces and functionally similar structures.

Keywords:
multiple alignmentproteinsstructural comparisons

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Last Updated: Jun 6, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
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Published on: July 14, 2015

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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:

  • Bioinformatics
  • Computational Biology
  • Structural Biology

Background:

  • Comparing 3D protein structures is crucial but computationally intensive.
  • Existing methods often require sequence information or strong assumptions.
  • There is a need for alignment methods that handle limited information.

Purpose of the Study:

  • To develop a novel computational approach for protein structural alignment using a data-mining strategy.
  • To identify conserved substructures, particularly in protein interfaces, irrespective of sequence order.
  • To compare the efficiency and effectiveness against existing protein structure comparison tools.

Main Methods:

  • Modeling protein structures as sets of 3D points, disregarding sequence order.
  • Employing geometric hashing to group spatially similar points.
  • Applying frequent pattern mining techniques to identify potential alignments from coincidence groups.
  • Utilizing a heuristic for extending identified alignments.

Main Results:

  • The algorithm successfully identified conserved substructures, especially within protein interfaces, without relying on sequence order.
  • It demonstrated the capability to detect functionally similar structures even within mixtures of dissimilar ones.
  • Computational performance was found to be competitive with, or superior to, existing tools.

Conclusions:

  • The proposed data-mining approach offers an effective and efficient solution for protein structural alignment with minimal prior information.
  • This method advances the field by enabling the discovery of structurally conserved regions independent of sequence.
  • The findings have implications for understanding protein function and evolution, particularly at interaction sites.