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Related Concept Videos

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...
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Globular and Fibrous Proteins

Many proteins can be classified into two distinct subtypes - globular or fibrous. These two types differ in their shapes and solubilities.
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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-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...
Structural Protein Function01:56

Structural Protein Function

Structural proteins are a category of proteins responsible for functions ranging from cell shape and movement to providing support to major structures such as bones, cartilage, hair, and muscles. This group includes proteins such as collagen, actin, myosin, and keratin.
Collagen, the most abundant protein in mammals, is found throughout the body. In connective tissue, such as skin, ligaments, and tendons, it provides tensile strength and elasticity.  In bones and teeth, it mineralizes to form...
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Structural Protein Function

Structural proteins are a category of proteins responsible for functions ranging from cell shape and movement to providing support to major structures such as bones, cartilage, hair, and muscles. This group includes proteins such as collagen, actin, myosin, and keratin.
Collagen, the most abundant protein in mammals, is found throughout the body. In connective tissue, such as skin, ligaments, and tendons, it provides tensile strength and elasticity.  In bones and teeth, it mineralizes to form...

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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

WildSpan: mining structured motifs from protein sequences.

Chen-Ming Hsu1, Chien-Yu Chen, Baw-Jhiune Liu

  • 1Department of Bio-Industrial Mechatronics Engineering, National Taiwan University, Taipei, 106, Taiwan. cychen@mars.csie.ntu.edu.tw.

Algorithms for Molecular Biology : AMB
|April 2, 2011
PubMed
Summary
This summary is machine-generated.

WildSpan efficiently discovers protein functional motifs (W-patterns) with large gaps. This algorithm improves protein sequence annotation and function prediction by effectively mining conserved residues separated by significant distances.

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Last Updated: Jun 3, 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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Peptide-based Identification of Functional Motifs and their Binding Partners
14:28

Peptide-based Identification of Functional Motifs and their Binding Partners

Published on: June 30, 2013

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Molecular Biology

Background:

  • Automatic motif extraction from biological sequences is crucial for molecular biology.
  • Discovering protein motifs with large numbers of wildcards (W-patterns) is challenging due to computational complexity.
  • Existing constraint models may reduce motif discovery accuracy.

Purpose of the Study:

  • To introduce an efficient algorithm, WildSpan, for discovering W-patterns in protein sequences.
  • To address the challenge of mining motifs with large, irregular gaps.
  • To improve large-scale sequence annotation and function prediction.

Main Methods:

  • Proposed a novel constraint model for W-patterns, which are structured motifs with pattern blocks and large gaps.
  • Developed the WildSpan algorithm incorporating pruning strategies to reduce mining cost.
  • Implemented two mining strategies: protein-based and family-based.

Main Results:

  • WildSpan efficiently identifies W-patterns with conserved residues separated by large distances.
  • Protein-based mining validated W-patterns against multiple sequence alignment for single protein characterization.
  • Family-based mining compared W-patterns with PROSITE patterns for protein function classification, demonstrating WildSpan's effectiveness and scalability.

Conclusions:

  • WildSpan is an efficient and effective tool for discovering protein functional signatures directly from sequences.
  • The proposed pruning strategy significantly enhances WildSpan's scalability.
  • W-patterns discovered by WildSpan provide valuable insights for protein sequence characterization.