Related Experiment Video
Updated: Oct 5, 2025
10:58
Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
Published on: July 25, 2013
17.2K
Heuristic algorithms in evolutionary computation and modular organization of biological macromolecules: Applications
Alexander V Spirov1,2, Ekaterina M Myasnikova3
1I. M. Sechenov Institute of Evolutionary Physiology and Biochemistry Russian Academy of Sciences, St. Petersburg, Russia.
Plos One
|January 27, 2022
Summary
Evolutionary computing methods can accelerate in vitro evolution experiments. By adapting genetic algorithm building block concepts to biological systems, researchers can enhance directed evolution efficiency for macromolecules.
Area of Science:
- Computer Science and Applied Mathematics
- Synthetic Biology
- Biotechnology
Background:
- Evolutionary computing (EC) utilizes nature-inspired optimization algorithms.
- EC methods, particularly genetic algorithms (GA), excel at identifying and combining 'building blocks' (BBs) for efficient search.
- In vitro evolution of biological macromolecules presents challenges analogous to EC search problems.
Purpose of the Study:
- To explore the application of EC principles to in vitro evolution.
- To adapt EC's 'building block' concept for directed evolution of biological macromolecules.
- To develop novel fitness functions and algorithms for enhanced in vitro evolution.
Main Methods:
- Extension of John Holland's Royal Roads fitness function to create Biological Royal Staircase (BioRS) functions.
- Development of heuristic algorithms inspired by EC's building block preservation strategies.
- Numerical testing of BioRS functions with heuristic algorithms for aptazyme evolution.
Main Results:
- BioRS functions effectively model in vitro evolution challenges for RNA-devices.
- Simple heuristic algorithms demonstrated high efficacy in preserving building blocks within BioRS.
- These algorithms proved highly effective for in vitro evolution approaches.
Conclusions:
- EC methods, especially those preserving building blocks, are suitable for in vitro evolution.
- The developed BioRS functions and heuristic algorithms can significantly improve efficiency.
- Implementation of these EC-inspired methods promises substantial time and resource savings in directed evolution experiments.
More Related Videos
Related Concept Videos
02:54Evolutionary Relationships through Genome Comparisons
6.4K
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
6.4K
02:31Synteny and Evolution
3.4K
John H. Renwick first coined the term “synteny” in 1971, which refers to the genes present on the same chromosomes, even if they are not genetically linked. The species with common ancestry tend to show conserved syntenic regions. Therefore, the concept of synteny is nowadays used to describe the evolutionary relationship between species.
Around 80 million years ago, the human and mice lineages diverged from the common ancestor. During the course of evolution, the ancestral...
Around 80 million years ago, the human and mice lineages diverged from the common ancestor. During the course of evolution, the ancestral...
3.4K
01:20Applications of Molecular Taxonomy
169
Molecular taxonomy has revolutionized the understanding and classification of bacteria, providing precise insights into their diversity, evolutionary relationships, and ecological roles. By utilizing molecular techniques such as DNA sequencing and fingerprinting, researchers have made significant strides in various fields related to bacterial studies.Resolving Taxonomic AmbiguitiesMolecular taxonomy has been instrumental in distinguishing closely related bacterial species initially thought to...
169
01:29Mechanistic Models: Compartment Models in Algorithms for Numerical Problem Solving
115
Mechanistic models play a crucial role in algorithms for numerical problem-solving, particularly in nonlinear mixed effects modeling (NMEM). These models aim to minimize specific objective functions by evaluating various parameter estimates, leading to the development of systematic algorithms. In some cases, linearization techniques approximate the model using linear equations.
In individual population analyses, different algorithms are employed, such as Cauchy's method, which uses a...
In individual population analyses, different algorithms are employed, such as Cauchy's method, which uses a...
115
02:05Gene Evolution - Fast or Slow?
7.5K
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...
In contrast, regions which code...
7.5K
01:28ATP and Macromolecule Synthesis
6.2K
Biological macromolecules are organic compounds, predominantly composed of carbon atoms. The carbon atoms are covalently bonded with hydrogen, oxygen, nitrogen, and other minor elements. There are four major biological macromolecule classes: carbohydrates, lipids, proteins, and nucleic acids.
Most macromolecules are composed of single subunits, or building blocks, called monomers. The monomers combine with each other using covalent bonds to form larger molecules known as polymers.
Conversion of...
Most macromolecules are composed of single subunits, or building blocks, called monomers. The monomers combine with each other using covalent bonds to form larger molecules known as polymers.
Conversion of...
6.2K