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Per-Unit Sequence Models

Per-Unit Sequence Models

An ideal Y-Y transformer, grounded through neutral impedances, displays per-unit sequence networks akin to those of a single-phase ideal transformer when subjected to balanced positive- or negative-sequence currents. These currents do not produce neutral currents, and their associated voltage drops.
Zero-sequence currents, which are identical in magnitude and phase, generate a neutral current, resulting in voltage drops across the neutral impedance and the low-voltage winding. If the...

Conservation of Protein Domains

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...

Conservation of Protein Domains Over Different Proteins

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...

Modeling with Differential Equations

Modeling with Differential Equations

Population dynamics can be described mathematically by considering the population size P(t) as a function of time. The rate of change of the population is then represented by the derivative of P(t). A simple assumption is that the rate of growth is proportional to the size of the population itself. This leads to an exponential growth model, where the population increases rapidly without bound. While this is a useful first approximation, it does not reflect realistic long-term...

Sequence Networks of Rotating Machines

Sequence Networks of Rotating Machines

A Y-connected synchronous generator, grounded through a neutral impedance, is designed to produce balanced internal phase voltages with only positive-sequence components. The generator's sequence networks include a source voltage that is exclusively in the positive-sequence network. The sequence components of line-to-ground voltages at the generator terminals illustrate this configuration.
Zero-sequence current induces a voltage drop across the generator's neutral impedance and other...

Conserved Binding Sites

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...

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Related Experiment Video

Updated: May 24, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

REvolver: modeling sequence evolution under domain constraints.

Tina Koestler¹, Arndt von Haeseler, Ingo Ebersberger

¹University of Vienna, Vienna, Austria. tina.koestler@univie.ac.at

Molecular Biology and Evolution

|March 3, 2012

Summary

REvolver simulates protein sequence evolution realistically, maintaining functional domains by using profile hidden Markov models (pHMMs). This approach preserves 92% of protein domains, a significant improvement over traditional methods.

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Design and Synthesis of a Reconfigurable DNA Accordion Rack

Design and Synthesis of a Reconfigurable DNA Accordion Rack

Published on: August 15, 2018

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Last Updated: May 24, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

Design and Synthesis of a Reconfigurable DNA Accordion Rack

Design and Synthesis of a Reconfigurable DNA Accordion Rack

Published on: August 15, 2018

Area of Science:

Computational Biology
Evolutionary Biology
Bioinformatics

Background:

Realistic simulation of protein sequence evolution is crucial for evolutionary studies.
Current simulators often fail to maintain protein structure and function due to independent site evolution.
Limited knowledge of evolutionary constraints hinders more accurate simulations.

Purpose of the Study:

To present REvolver, a novel program for simulating protein sequence evolution with realistic constraints.
To enable the maintenance of evolutionarily stable sequence characteristics, such as functional domains.
To facilitate large-scale, proteome-wide simulation studies.

Main Methods:

REvolver utilizes profile hidden Markov models (pHMMs) to parameterize site-specific models of sequence evolution.
pHMMs are derived from alignments of homologous proteins to capture conservation and variation patterns.
The program was used to evolve the entire human proteome and analyze domain preservation.

Main Results:

REvolver preserved 92% of Pfam domains in simulated human proteome evolution.
Traditional models of amino acid sequence evolution preserved only 15% of domains.
The tool successfully simulated protein family evolution with user-defined domain architectures.

Conclusions:

REvolver significantly advances realistic simulation of protein sequence evolution on a proteome-wide scale.
The program's ability to maintain protein domains is a key improvement over existing methods.
REvolver facilitates studies on evolutionary constraints and protein family evolution.