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Related Concept Videos

Structures of Solids02:22

Structures of Solids

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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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Structural Isomerism02:34

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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.
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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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Bioinformatics Resources for the Study of Glycan-Mediated Protein Interactions
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Chemoinformatics and structural bioinformatics in OCaml.

Francois Berenger1, Kam Y J Zhang2, Yoshihiro Yamanishi3,4

  • 1Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, Iizuka, Fukuoka, Japan. beren314@bio.kyutech.ac.jp.

Journal of Cheminformatics
|February 6, 2019
PubMed
Summary
This summary is machine-generated.

OCaml is a powerful functional programming language ideal for developing chemoinformatics and structural bioinformatics software. Its features enable efficient prototyping and high-performance scientific applications.

Keywords:
Bisector treeChemoinformaticsFunctional programmingOCamlOpen sourceScientific softwareSoftware prototypingStructural bioinformatics

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Area of Science:

  • Computational chemistry
  • Bioinformatics
  • Software development

Background:

  • OCaml is a functional programming language with strong static types, Hindley-Milner type inference, and garbage collection.
  • This article details experiences prototyping chemoinformatics and structural bioinformatics software using OCaml.

Purpose of the Study:

  • To introduce OCaml to chemoinformaticians.
  • To demonstrate OCaml's suitability for scientific software development.
  • To provide resources for adopting OCaml in bioinformatics.

Main Methods:

  • Introduction to OCaml language features relevant to scientific computing.
  • Code examples and demonstrations of OCaml in action.
  • Review of existing OCaml-based scientific software and libraries.

Main Results:

  • OCaml offers efficient prototyping capabilities for scientific software.
  • Demonstrated parallelization and performance of OCaml programs.
  • Identified useful open-source libraries and tools for chemoinformatics.

Conclusions:

  • OCaml is a preferred language for method development in chemoinformatics.
  • OCaml facilitates the creation of robust structural bioinformatics tools.
  • The language's features support high-performance scientific computing.