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

Entropy02:39

Entropy

36.2K
Salt particles that have dissolved in water never spontaneously come back together in solution to reform solid particles. Moreover, a gas that has expanded in a vacuum remains dispersed and never spontaneously reassembles. The unidirectional nature of these phenomena is the result of a thermodynamic state function called entropy (S). Entropy is the measure of the extent to which the energy is dispersed throughout a system, or in other words, it is proportional to the degree of disorder of a...
36.2K
Entropy01:18

Entropy

3.6K
The first law of thermodynamics is quantitatively formulated via an equation relating the internal energy of a system, the heat exchanged by it, and the work done on it. A quantitative formulation of the second law of thermodynamics leads to defining a state function, the entropy.
When an ideal gas expands isothermally, the disorder in the gas increases. From the molecular perspective, the gas molecules have more volume to move around in.
Consider an infinitesimal step in the expansion, which...
3.6K
Standard Entropy Change for a Reaction03:00

Standard Entropy Change for a Reaction

24.9K
Entropy is a state function, so the standard entropy change for a chemical reaction (ΔS°rxn) can be calculated from the difference in standard entropy between the products and the reactants.
24.9K
Conservative Site-specific Recombination and Phase Variation02:53

Conservative Site-specific Recombination and Phase Variation

6.8K
Because the DNA segments are cut and reorganized in a direction-specific manner, site-specific recombination has emerged as an efficient genetic engineering technique. Flippase and Cyclization recombinases or Flp and Cre, respectively, are two members of the tyrosine recombinase family derived from bacteriophages, that are used to mediate site-specific DNA insertions, deletions, and targeted expression of proteins in mammalian cell lines.
The recognition sites for Cre recombinase called LoxP...
6.8K
What is Variation?01:14

What is Variation?

18.6K
Apart from the measures of central tendency, distribution, outliers, and the changing characteristics of data with time, an important characteristic of any data set is its variation or spread. In some data sets, the data values are concentrated closely near the mean; in others, the data values are more widely spread out from the mean.
The range, standard deviation, standard error, and variance are the different measures of variation.
Range: The range is the difference between its maximum and...
18.6K
Entropy and Solvation02:05

Entropy and Solvation

8.4K
The process of surrounding a solute with solvent is called solvation. It involves evenly distributing the solute within the solvent. The rule of thumb for determining a solvent for a given compound is that like dissolves like. A good solvent has molecular characteristics similar to those of the compound to be dissolved. For example, polar solutions dissolve polar solutes, and apolar solvents dissolve apolar solutes. A polar solvent is a solvent that has a high dielectric constant (ϵ...
8.4K

You might also read

Related Articles

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

Sort by
Same author

PyVADesign: a python-based cloning tool for one-step generation of large mutant libraries.

Bioinformatics (Oxford, England)·2025
Same author

Corrigendum to "Impact of cancer-associated mutations in CC chemokine receptor 2 on receptor function and antagonism" [Biochem. Pharmacol. 208 (2023) 115399].

Biochemical pharmacology·2023
Same author

Papyrus: a large-scale curated dataset aimed at bioactivity predictions.

Journal of cheminformatics·2023
Same author

Impact of cancer-associated mutations in CC chemokine receptor 2 on receptor function and antagonism.

Biochemical pharmacology·2022
Same author

Pan-cancer functional analysis of somatic mutations in G protein-coupled receptors.

Scientific reports·2022
Same author

GenUI: interactive and extensible open source software platform for de novo molecular generation and cheminformatics.

Journal of cheminformatics·2021
Same journal

OmicsTransformer: Self-Supervised Masked Consistency and Uncertainty-Aware Fusion for Robust Multi-Omics Prediction.

Bioinformatics (Oxford, England)·2026
Same journal

Computational Tool Choice Impacts CRISPR Spacer-Proto spacer Detection.

Bioinformatics (Oxford, England)·2026
Same journal

ARISE: RNA-Anchored Shared-Edge Topology and Hierarchical Fusion for Spatial Multi-Omics Integration.

Bioinformatics (Oxford, England)·2026
Same journal

Interactive exploration of biobank-scale ancestral recombination graphs with Lorax.

Bioinformatics (Oxford, England)·2026
Same journal

PepMCP: A Graph-Based Membrane Contact Probability Predictor for Membrane-Lytic Antimicrobial Peptides.

Bioinformatics (Oxford, England)·2026
Same journal

ARGscape: A modular, interactive tool for manipulation of spatiotemporal ancestral recombination graphs.

Bioinformatics (Oxford, England)·2026
See all related articles

Related Experiment Video

Updated: Feb 6, 2026

Optimization for Sequencing and Analysis of Degraded FFPE-RNA Samples
07:30

Optimization for Sequencing and Analysis of Degraded FFPE-RNA Samples

Published on: June 8, 2020

12.8K

PyTEA-O: a Python implementation of Two-Entropies Analysis for protein sequence variation analysis.

R C M Kuin1, A T Julian2, J Chander2

  • 1Computational Drug Discovery, Division of Medicinal Chemistry, Leiden Academic Centre of Drug Research, Leiden University, 2333 CC Leiden, The Netherlands.

Bioinformatics (Oxford, England)
|February 4, 2026
PubMed
Summary
This summary is machine-generated.

PyTEA-O is a new Python tool for analyzing protein sequence variation. It helps identify key residues influencing protein function and substrate affinity, aiding drug discovery and protein engineering.

More Related Videos

An Integrated Approach for Microprotein Identification and Sequence Analysis
09:37

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

4.0K
Comparative Lesions Analysis Through a Targeted Sequencing Approach
08:16

Comparative Lesions Analysis Through a Targeted Sequencing Approach

Published on: November 5, 2019

7.3K

Related Experiment Videos

Last Updated: Feb 6, 2026

Optimization for Sequencing and Analysis of Degraded FFPE-RNA Samples
07:30

Optimization for Sequencing and Analysis of Degraded FFPE-RNA Samples

Published on: June 8, 2020

12.8K
An Integrated Approach for Microprotein Identification and Sequence Analysis
09:37

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

4.0K
Comparative Lesions Analysis Through a Targeted Sequencing Approach
08:16

Comparative Lesions Analysis Through a Targeted Sequencing Approach

Published on: November 5, 2019

7.3K

Area of Science:

  • Biochemistry and Molecular Biology
  • Computational Biology
  • Structural Biology

Background:

  • Protein sequence variation analysis is crucial for drug discovery and protein engineering.
  • Existing computational tools often lack consideration of amino acid properties, flexibility, source code accessibility, or compatibility with small multiple sequence alignments (MSAs).

Purpose of the Study:

  • To address limitations of existing tools, this study introduces PyTEA-O, a user-friendly Python implementation of Two-Entropies Analysis.
  • The goal is to facilitate the analysis of protein sequence variation and identify residues critical for protein function specificity.

Main Methods:

  • PyTEA-O utilizes Python for analyzing multiple sequence alignments (MSAs).
  • It generates modifiable and intuitive visualizations to aid users in screening for residues of interest.
  • A scoring approach is employed to identify alignment positions with distinct physicochemical properties.

Main Results:

  • PyTEA-O provides a powerful tool for sequence variability analysis through visualizations and scoring.
  • A case study on deubiquitinase OTUD7B (Cezanne) identified a crucial position modulating substrate affinity.
  • The tool successfully demonstrates its capability in pinpointing functionally significant residues.

Conclusions:

  • PyTEA-O offers an accessible and effective solution for protein sequence variation analysis.
  • The tool supports drug discovery and protein engineering by identifying key residues that modulate protein function and interactions.
  • PyTEA-O is available as open-source software with archived data for reproducibility.