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Related Concept Videos

Conserved Binding Sites01:49

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...
Conserved Binding Sites01:49

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

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...
Conservation of Protein Domains02:26

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...
Conformations of Cycloalkanes02:29

Conformations of Cycloalkanes

Adolf von Baeyer attempted to explain the instabilities of small and large cycloalkane rings using the concept of angle strain — the strain caused by the deviation of bond angles from the ideal 109.5° tetrahedral value for sp3  hybridized carbons. However, while cyclopropane and cyclobutane are strained, as expected from their highly compressed bond angles, cyclopentane is more strained than predicted, and cyclohexane is virtually strain-free. Hence, Baeyer’s theory that was based on the...
Multi-species Conserved Sequences02:51

Multi-species Conserved Sequences

Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale  studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved DNA...

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Updated: Jul 15, 2026

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
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Conformational coverage by a genetic algorithm: saturation of conformational space.

Todor Pavlov1, Milen Todorov, Galina Stoyanova

  • 1Laboratory of Mathematical Chemistry, University Prof. As. Zlatarov, 8010 Bourgas, Bulgaria.

Journal of Chemical Information and Modeling
|May 1, 2007
PubMed
Summary

Molecular modeling accuracy improves by analyzing diverse, energetically reasonable conformers, not just minimum energy ones. This study refines evolutionary algorithms for stable conformational distributions, enhancing chemical modeling reliability.

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Area of Science:

  • Computational Chemistry
  • Cheminformatics

Background:

  • Traditional molecular modeling relies on minimum energy conformers, which may not represent the molecule's true behavior or activity.
  • Significant variations in geometric and electronic properties exist across energetically reasonable conformers.
  • The selection of active conformers is crucial for successful molecular modeling, akin to selecting molecular descriptors.

Purpose of the Study:

  • To present an improved evolutionary algorithm for conformer generation.
  • To minimize the sensitivity of conformer distributions to smoothing parameters.
  • To enhance the reproducibility of conformer distributions generated by genetic algorithms (GA).

Main Methods:

  • Development of an improved evolutionary algorithm for conformer generation.
  • Application of a 'saturation' procedure to achieve stable conformational distributions.
  • Utilizing genetic algorithms (GA) for conformational analysis.

Main Results:

  • The improved algorithm minimizes sensitivity to smoothing parameters and enhances reproducibility.
  • A stable conformational distribution is achieved with an optimal number of conformers.
  • The saturation procedure ensures conformational distributions are not significantly altered by adding more conformers.

Conclusions:

  • Accurate molecular modeling requires considering a representative set of conformers, not just the lowest energy ones.
  • The developed evolutionary algorithm and saturation procedure improve the reliability and adequacy of conformational analysis.
  • This approach enhances the accuracy of molecular similarity assessments.