Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Conserved Binding Sites01:49

Conserved Binding Sites

4.2K
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...
4.2K
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

4.8K
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...
4.8K
Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

10.9K
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...
10.9K
Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

7.1K
The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
7.1K
Allosteric Proteins-ATCase01:19

Allosteric Proteins-ATCase

5.7K
Binding sites linkages can regulate a protein's function.  For example, enzyme activity is often regulated through a feedback mechanism where the end product of the biochemical process serves as an inhibitor.
Aspartate transcarbamoylase (ATCase) is a cytosolic enzyme that catalyzes the condensation of L-aspartate and carbamoyl phosphate to  N-carbamoyl-L-aspartate. This reaction is the first step in pyrimidine biosynthesis. UTP and CTP, the end products of the pyrimidine synthesis...
5.7K
Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

2.5K
Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order...
2.5K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Cold Agglutinin-Mediated Hemolysis as an Extrapulmonary Manifestation of Mycoplasma pneumoniae Infection: A Case Report.

Cureus·2026
Same author

Trends in substitution models of protein evolution for phylogenetic inference.

Molecular phylogenetics and evolution·2025
Same author

Empirical substitution models of protein evolution: database, relationships, and modeling considerations.

Database : the journal of biological databases and curation·2025
Same author

Forecasting protein evolution by integrating birth-death population models with structurally constrained substitution models.

eLife·2025
Same author

Heterogeneous Evolution Among SARS-CoV-2 Genes and Variants of Concern.

Journal of medical virology·2025
Same author

Molecular Evolution and Phylogeography of the Crimean-Congo Hemorrhagic Fever Virus.

Viruses·2025

Related Experiment Video

Updated: Jul 2, 2025

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

17.1K

Selection among site-dependent structurally constrained substitution models of protein evolution by approximate

David Ferreiro1,2, Catarina Branco1,2, Miguel Arenas1,2

  • 1CINBIO, Universidade de Vigo, 36310 Vigo, Spain.

Bioinformatics (Oxford, England)
|February 19, 2024
PubMed
Summary

We developed ProteinModelerABC for selecting protein evolution models. This tool accurately selects among structurally constrained substitution (SCS) and empirical models, improving phylogenetic inferences.

More Related Videos

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

7.3K
Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group
07:49

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Published on: August 16, 2017

7.1K

Related Experiment Videos

Last Updated: Jul 2, 2025

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

17.1K
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

7.3K
Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group
07:49

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Published on: August 16, 2017

7.1K

Area of Science:

  • Computational Biology
  • Molecular Evolution
  • Bioinformatics

Background:

  • Accurate phylogenetic inference relies on appropriate molecular evolution models.
  • Traditional empirical substitution models for proteins have limitations and unrealistic assumptions.
  • Structurally constrained substitution (SCS) models offer greater realism, particularly site-dependent evolution, but are complex to implement.

Purpose of the Study:

  • To present a novel computational framework, ProteinModelerABC, for selecting among protein substitution models.
  • To implement approximate Bayesian computation (ABC) for model selection, incorporating both empirical and site-dependent SCS models.
  • To evaluate the accuracy of the ABC approach for model selection using simulated and real protein family data.

Main Methods:

  • Developed ProteinModelerABC, a computational framework implementing approximate Bayesian computation (ABC).
  • Integrated diverse empirical and site-dependent structurally constrained substitution (SCS) models within the framework.
  • Employed ABC with and without regression adjustments for model selection, validated using extensive simulated data.

Main Results:

  • The ProteinModelerABC framework demonstrates acceptable accuracy in selecting among SCS and empirical protein evolution models.
  • Analysis of diverse protein families revealed that SCS models provide a better fit compared to the best-fitting empirical models.
  • The method successfully handles the complexity of site-dependent evolution inherent in SCS models.

Conclusions:

  • ProteinModelerABC offers a robust and accurate method for selecting appropriate protein substitution models.
  • Structurally constrained substitution models, particularly site-dependent ones, are superior to empirical models for protein evolution analysis.
  • The developed framework facilitates more reliable phylogenetic inferences in molecular evolution studies.