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Related Concept Videos

Ligand Binding and Linkage00:49

Ligand Binding and Linkage

Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence the...
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence the...
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...
Covalently Linked Protein Regulators02:04

Covalently Linked Protein Regulators

Proteins can undergo many types of post-translational modifications, often in response to changes in their environment. These modifications play an important role in the function and stability of these proteins. Covalently linked molecules include functional groups, such as methyl, acetyl, and phosphate groups, and also small proteins, such as ubiquitin. There are around 200 different types of covalent regulators that have been identified.
These groups modify specific amino acids in a protein.

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Related Experiment Video

Updated: Jun 28, 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

Inferring molecular function: contributions from functional linkages.

Arturo Medrano-Soto1, Debnath Pal, David Eisenberg

  • 1Howard Hughes Medical Institute (HHMI), 675C. E. Young Drive South, Los Angeles, CA 90095, USA.

Trends in Genetics : TIG
|October 28, 2008
PubMed
Summary
This summary is machine-generated.

Automated gene function prediction using functional linkages improves accuracy by 8% and enriches descriptions for 34% of assignments. This method is supported by over 80% of biochemical literature for unannotated proteins.

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Area of Science:

  • Biomedical Science
  • Genomics
  • Bioinformatics

Background:

  • High-throughput sequencing and structure determination generate vast amounts of data.
  • Functional annotation of genes and proteins remains a significant bottleneck in biomedical research.
  • Accurate functional annotation is crucial for understanding biological processes and disease mechanisms.

Purpose of the Study:

  • To develop and evaluate an automated method for inferring molecular function using gene functional linkages.
  • To assess the impact of this automated approach on the accuracy and richness of functional assignments.
  • To validate the automated inferences against existing biochemical literature.

Main Methods:

  • Utilized functional linkages among genes to infer molecular function.
  • Quantified the improvement in accuracy for functional assignments.
  • Measured the enrichment of functional descriptions in top assignments.
  • Validated automated inferences using biochemical literature data.

Main Results:

  • Automated inference of molecular function using functional linkages increased assignment accuracy by over 8%.
  • Functional descriptions were enriched in over 34% of top assignments.
  • Over 80% of automated inferences for previously unannotated proteins were supported by biochemical literature.

Conclusions:

  • Incorporating functional linkages into protein annotation significantly enhances accuracy and descriptive richness.
  • Automated inference provides a reliable and literature-supported approach to overcome functional annotation bottlenecks.
  • This strategy offers a scalable solution for annotating large datasets in biomedical science.