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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...
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 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...
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...
Multi-species Conserved Sequences02:51

Multi-species Conserved Sequences

Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale  studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved DNA...
Structure of Conjugated Dienes01:16

Structure of Conjugated Dienes

Introduction
Conjugated dienes are compounds characterized by the presence of alternating double and single bonds. In a conjugated system like 1,3-butadiene, the unhybridized 2p orbital on each carbon overlaps continuously, allowing the π electrons to be delocalized across the entire molecule. In contrast, this type of overlap does not occur in cumulated and isolated dienes, such as 2,3-pentadiene and 1,4-pentadiene, respectively. Instead, the π electrons remain localized between the double...

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Related Experiment Video

Updated: Jun 12, 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

dConsensus: a tool for displaying domain assignments by multiple structure-based algorithms and for construction of a

Kieran Alden1, Stella Veretnik, Philip E Bourne

  • 1York Centre for Complex Systems Analysis (YCCSA), University of York, Heslington, York, YO10 5DD, UK.

BMC Bioinformatics
|June 10, 2010
PubMed
Summary

dConsensus integrates multiple protein domain assignment algorithms to create a consensus view. This tool aids in understanding protein structure and evolutionary relationships by combining algorithmic and expert assignments.

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Last Updated: Jun 12, 2026

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

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Published on: July 14, 2015

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16:24

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

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

Area of Science:

  • Structural biology
  • Bioinformatics

Background:

  • Protein domain partitioning is crucial for classification, functional, and evolutionary studies.
  • High-throughput structure determination necessitates automated domain assignment methods.
  • Existing algorithmic methods have varying strengths and weaknesses, lacking a unified comparison platform.

Purpose of the Study:

  • To develop a resource for comparing and consolidating protein domain assignments from multiple algorithmic methods.
  • To generate a consensus domain assignment with a reliability score.
  • To provide insights into protein structure partitioning and algorithm tendencies.

Main Methods:

  • Integration of domain assignments from seven structure-based algorithms (PDP, PUU, DomainParser2, NCBI method, DHcL, DDomains, Dodis) and expert methods.
  • Development of a web resource (dConsensus) for displaying and comparing these assignments.
  • Generation of consensus assignments using simple averaging or weighted contributions based on prior performance.

Main Results:

  • dConsensus provides a unified platform for analyzing protein domain assignments from multiple algorithms.
  • Consensus assignments are generated, offering a potentially more accurate view of protein structure partitioning.
  • Analysis of secondary structure around domain boundaries is available.

Conclusions:

  • dConsensus enables comprehensive protein domain assignment by aggregating seven algorithmic methods.
  • It facilitates comparative analysis, offering insights into protein structure, evolution, and function.
  • Users can gain a deeper understanding by comparing consensus and individual method assignments.