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Related Concept Videos

Structural Isomerism02:34

Structural Isomerism

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Isomerism in Complexes
Isomers are different chemical species that have the same chemical formula. Structural isomerism of coordination compounds can be divided into two subcategories, the linkage isomers and coordination-sphere isomers.
Linkage isomers occur when the coordination compound contains a ligand that can bind to the transition metal center through two different atoms. For example, the CN− ligand can bind through the carbon atom or through the nitrogen atom. Similarly, SCN− can...
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Solids in which the atoms, ions, or molecules are arranged in a definite repeating pattern are known as crystalline solids. Metals and ionic compounds typically form ordered, crystalline solids. A crystalline solid has a precise melting temperature because each atom or molecule of the same type is held in place with the same forces or energy. Amorphous solids or non-crystalline solids (or, sometimes, glasses) which lack an ordered internal structure and are randomly arranged. Substances that...
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Structure of Lipids03:38

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Lipids include a diverse group of compounds that are largely nonpolar in nature. This is because they are hydrocarbons that include mostly nonpolar carbon-carbon or carbon-hydrogen bonds. Non-polar molecules are hydrophobic (“water fearing”), or insoluble in water. Lipids perform many different functions in a cell. Cells store energy for long-term use in the form of fats. Lipids also provide insulation from the environment for plants and animals. For example, they help keep aquatic...
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Viral Structure00:56

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Viruses are extraordinarily diverse in shape and size, but they all have several structural features in common. All viruses have a core that contains a DNA- or RNA-based genome. The core is surrounded by a protective coat of proteins called the capsid. The capsid is composed of subunits called capsomeres. The capsid and genome-containing core are together known as the nucleocapsid.
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Antibody Structure01:10

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Antibodies, also known as immunoglobulins (Ig), are essential players of the adaptive immune system. These antigen-binding proteins are produced by B cells and make up 20 percent of the total blood plasma by weight. In mammals, antibodies fall into five different classes, which each elicits a different biological response upon antigen binding.
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Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
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The Application of Open Searching-based Approaches for the Identification of Acinetobacter baumannii O-linked Glycopeptides
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Enumeration Method for Structural Isomers Containing User-Defined Structures Based on Breadth-First Search Approach.

Jira Jindalertudomdee1, Morihiro Hayashida1, Tatsuya Akutsu1

  • 1Laboratory of Mathematical Bioinformatics, Bioinformatics Center, Institute for Chemical Research, Kyoto University , Kyoto, Japan .

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
|June 28, 2016
PubMed
Summary
This summary is machine-generated.

A new algorithm, BfsStructEnum, efficiently enumerates chemical structures based on defined cyclic components and chemical formulas. This method significantly outperforms existing tools like MOLGEN 5.0 in speed while generating comparable results for drug discovery.

Keywords:
breadth-first searchenumerationstructural isomer

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Area of Science:

  • Computational chemistry
  • Cheminformatics
  • Drug discovery

Background:

  • Chemical structure enumeration is crucial for discovering new compounds and drugs.
  • Defining specific cyclic structures and chemical formulas are common enumeration constraints.
  • Existing methods may face performance limitations in complex enumerations.

Purpose of the Study:

  • To introduce a novel and efficient algorithm, BfsStructEnum, for enumerating chemical structures.
  • To enable users to specify desired cyclic structures for enumeration.
  • To compare the performance and efficiency of BfsStructEnum against established structure generators.

Main Methods:

  • Developed the BfsStructEnum algorithm for chemical structure enumeration.
  • Implemented a graph compression technique, representing cyclic structures as single nodes and compounds as tree structures.
  • Compared BfsStructEnum with MOLGEN 5.0 in terms of enumerated structure count and computation time.

Main Results:

  • BfsStructEnum successfully enumerates nonredundant chemical compounds based on user-defined cyclic structures and chemical formulas.
  • The algorithm achieves comparable enumeration results to MOLGEN 5.0.
  • BfsStructEnum demonstrates significantly faster computation times compared to MOLGEN 5.0 for equivalent enumeration tasks.

Conclusions:

  • BfsStructEnum offers a more efficient approach to chemical structure enumeration.
  • The algorithm's efficiency stems from its novel representation of cyclic structures and compounds.
  • BfsStructEnum presents a valuable tool for accelerating drug discovery and chemical structure elucidation.