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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 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...
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...
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...

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Related Experiment Video

Updated: Jun 13, 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

Predicting conserved protein motifs with Sub-HMMs.

Kevin Horan1, Christian R Shelton, Thomas Girke

  • 1Department of Computer Science and Engineering, University of California Riverside, Riverside, California, USA.

BMC Bioinformatics
|April 28, 2010
PubMed
Summary
This summary is machine-generated.

This study introduces sub-hidden Markov models (sub-HMMs) to efficiently identify conserved functional motifs within protein families. These sub-HMMs enhance protein analysis by pinpointing critical sequence features and enabling novel similarity searches.

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Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
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Published on: January 26, 2024

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Structural Biology

Background:

  • Profile hidden Markov models (HMMs) are effective for modeling conserved protein family regions.
  • A key limitation is the difficulty in identifying shorter, functionally critical sub-features within these models.

Purpose of the Study:

  • To develop and validate a method for extracting information-rich sub-regions from profile HMMs.
  • To identify conserved functional motifs and link protein domains based on shared sub-HMMs.

Main Methods:

  • Developed a novel method to extract sub-HMMs from protein family profile HMMs.
  • Applied the method to the Pfam domain database.
  • Validated predictions using PROSITE and CSA databases.

Main Results:

  • Successfully predicted a comprehensive set of sub-HMMs, identifying 46,768 novel conserved regions.
  • Confirmed the method's efficiency in predicting known functional motifs and residues.
  • Linked 461 Pfam domains through common sub-HMMs and demonstrated potential for localized similarity searches.

Conclusions:

  • Sub-HMMs expand the utility of profile HMMs for motif discovery and identification of functionally relevant residues.
  • This approach facilitates highly localized sequence similarity searches focusing on short conserved features.
  • The generated motif data serves as a valuable resource for future protein function characterization.