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

Amino acids03:42

Amino acids

106.6K
Amino acids are the monomers that comprise proteins. Each amino acid has the same fundamental structure, which consists of a central carbon atom, or the alpha (α) carbon, bonded to an amino group (NH2), a carboxyl group (COOH), and to a hydrogen atom. Every amino acid also has another atom or group of atoms bonded to the central atom known as the R group. There are 20 common amino acids present in proteins, each with a different R group. Variation in the amino acid sequence is responsible for...
106.6K
Amino Acid Catabolism01:18

Amino Acid Catabolism

1.3K
Microorganisms rely on proteins as an essential carbon and energy source, particularly in environments with limited polysaccharides or lipids. However, proteins are too large to cross the plasma membrane unaided, necessitating enzymatic degradation. Microbes secrete extracellular proteases and peptidases that hydrolyze proteins into peptides, which can then be transported across the membrane. Once inside the cell, intracellular proteases degrade these peptides into free amino acids, which...
1.3K
Amino Acid Biosynthetic Pathways01:29

Amino Acid Biosynthetic Pathways

1.4K
Amino acid biosynthesis is essential for cell growth, protein synthesis, and metabolic regulation. Cells generate essential and non-essential amino acids from metabolic intermediates to sustain vital biological functions. These intermediates originate from key metabolic pathways: glycolysis, the tricarboxylic acid (TCA) cycle, and the pentose phosphate pathway. Important precursors include α-ketoglutarate, pyruvate, oxaloacetate, phosphoenolpyruvate, and erythrose-4-phosphate, which...
1.4K
Phase II Reactions: Sulfation and Conjugation with α-Amino Acids01:19

Phase II Reactions: Sulfation and Conjugation with α-Amino Acids

1.0K
Sulfation and α-amino acid conjugation are two critical biotransformation reactions in drug metabolism. Sulfation, a phase II biotransformation reaction, involves adding a polar sulfate group to a drug, enhancing its water solubility and promoting excretion. This process can either co-occur with or occur independently of glucuronidation. Nonmicrosomal sulfotransferase enzymes catalyze the process. The reaction involves 3'-phosphoadenosine-5'-phosphosulfate or PAPS coenzyme...
1.0K
pH Scale02:41

pH Scale

80.5K
Hydronium and hydroxide ions are present both in pure water and in all aqueous solutions, and their concentrations are inversely proportional as determined by the ion product of water (Kw). The concentrations of these ions in a solution are often critical determinants of the solution’s properties and the chemical behaviors of its other solutes. Two different solutions can differ in their hydronium or hydroxide ion concentrations by a million, billion, or even trillion times. A common means of...
80.5K
Fischer Projections02:18

Fischer Projections

16.7K
Learning to draw Fischer projections of molecules and understanding their relevance plays a crucial role in the visual depiction of organic molecules. A Fischer projection is a two-dimensional projection on a planar surface to simplify the three-dimensional wedge–dash representation of molecules. This is especially helpful in the case of molecules with multiple chiral centers that can be difficult to draw. Here, all the bonds of interest are represented as horizontal or vertical lines. While...
16.7K

You might also read

Related Articles

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

Sort by
Same author

PolyDeep Advance 3: Randomized Clinical Trial comparing PolyDeep-assisted and conventional colonoscopy for adenoma detection rate in a colorectal cancer screening program.

Endoscopy·2026
Same author

Updates and validation of the Compi RNA-seq pipeline with a case study in Alzheimer's disease.

Journal of integrative bioinformatics·2026
Same author

PIBAdb: a public cohort of multimodal colonoscopy videos and images including polyps with histological information.

Computer methods and programs in biomedicine·2026
Same author

Clinical Evaluation of PolyDeep, A Computer-Aided Detection System: A Multicenter Randomized Tandem Colonoscopy Trial.

Diagnostics (Basel, Switzerland)·2025
Same author

Continent-wide differentiation of fitness traits and patterns of climate adaptation among European populations of <i>Drosophila melanogaster</i>.

Evolution letters·2025
Same author

Long-Term Impact of the Largest Environmental Disaster in Latin America (Fundão Dam Failure) on Microbial Communities in Lakes of the Doce River Basin, Brazil.

Environmental microbiology·2025

Related Experiment Video

Updated: Feb 15, 2026

Visualizing Visual Adaptation
04:43

Visualizing Visual Adaptation

Published on: April 24, 2017

9.6K

Large Scale Analyses and Visualization of Adaptive Amino Acid Changes Projects.

Noé Vázquez1,2, Cristina P Vieira3,4, Bárbara S R Amorim3,5

  • 1ESEI - Escuela Superior de Ingeniería Informática, Edificio Politécnico, Universidade de Vigo, Campus Universitario As Lagoas s/n, 32004, Ourense, Spain.

Interdisciplinary Sciences, Computational Life Sciences
|February 1, 2018
PubMed
Summary

New tools simplify identifying adaptive amino acid changes in protein sequences. The B+ database stores analysis projects, enabling large-scale studies and data reuse for evolutionary insights.

Keywords:
ADOPSB+ databaseOpen dataPositive selection

More Related Videos

Bioorthogonal Chemical Imaging of Cell Metabolism Regulated by Aromatic Amino Acids
10:42

Bioorthogonal Chemical Imaging of Cell Metabolism Regulated by Aromatic Amino Acids

Published on: May 12, 2023

1.6K
Curation of Computational Chemical Libraries Demonstrated with Alpha-Amino Acids
08:21

Curation of Computational Chemical Libraries Demonstrated with Alpha-Amino Acids

Published on: April 13, 2022

3.1K

Related Experiment Videos

Last Updated: Feb 15, 2026

Visualizing Visual Adaptation
04:43

Visualizing Visual Adaptation

Published on: April 24, 2017

9.6K
Bioorthogonal Chemical Imaging of Cell Metabolism Regulated by Aromatic Amino Acids
10:42

Bioorthogonal Chemical Imaging of Cell Metabolism Regulated by Aromatic Amino Acids

Published on: May 12, 2023

1.6K
Curation of Computational Chemical Libraries Demonstrated with Alpha-Amino Acids
08:21

Curation of Computational Chemical Libraries Demonstrated with Alpha-Amino Acids

Published on: April 13, 2022

3.1K

Area of Science:

  • Evolutionary Biology
  • Bioinformatics
  • Computational Biology

Background:

  • Identifying adaptive amino acid changes in proteins is crucial for understanding evolution.
  • Maximum-likelihood methods using codon substitution models (e.g., codeml) are standard but data-intensive.
  • Existing tools like BDBM and ADOPS streamline data collection and site inference.

Purpose of the Study:

  • To address the limitation of ADOPS lacking a batch option for large-scale analyses.
  • To introduce the B+ database for storing and accessing ADOPS projects.
  • To facilitate large-scale evolutionary studies and promote data sharing.

Main Methods:

  • Development of the B+ database as a repository for ADOPS projects.
  • Implementation of an interface for browsing ADOPS project data without downloading.
  • Leveraging existing tools (BDBM, ADOPS) for data collection and site inference.

Main Results:

  • The B+ database provides a centralized repository for ADOPS analyses.
  • Users can access and explore ADOPS project data through the B+ interface.
  • The system supports the analysis of hundreds or thousands of sequence files by enabling large-scale projects.

Conclusions:

  • The B+ database enhances the scalability of adaptive amino acid change detection.
  • It ensures results repeatability and promotes data reuse, saving significant time.
  • Facilitates further exploration and analysis of evolutionary data.