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Model[Molecule, Protein, Antibody]

Model information for a Y-shaped immune component that targets a specific antigen.

Organizational Information

    Name

    Name of this Object.
    Format: Single
    Class: String
    Programmatic Pattern: _String
    Pattern Description: A string.

    ID

    ID of this Object.
    Format: Single
    Class: String
    Programmatic Pattern: _String
    Pattern Description: The ID of this object.

    Object

    Object of this Object.
    Format: Single
    Class: Expression
    Programmatic Pattern: Model[Molecule, Protein, Antibody, _String]
    Pattern Description: The object reference of this object.

    Type

    Type of this Object.
    Format: Single
    Class: Expression

    Notebook

    Notebook this object belongs to.
    Format: Single
    Class: Link
    Programmatic Pattern: _Link
    Pattern Description: An object of that matches ObjectP[Object[LaboratoryNotebook]].

    Synonyms

    List of possible alternative names this model goes by.
    Format: Multiple
    Class: String
    Programmatic Pattern: _String

    Authors

    The people who created this model.
    Format: Multiple
    Class: Link
    Programmatic Pattern: _Link
    Relation: Object[User]

    Molecule

    The chemical structure that represents this molecule.
    Format: Single
    Class: Expression
    Programmatic Pattern: MoleculeP | _?StructureQ | _?StrandQ

    UNII

    Unique Ingredient Identifier of this molecule, as given by the unified identification scheme of the FDA.
    Format: Single
    Class: String
    Programmatic Pattern: _String

    InChI

    The International Chemical Identifer (InChI) that uniquely identifies this molecule.
    Format: Single
    Class: String
    Programmatic Pattern: InChIP

    InChIKey

    The hashed version of the International Chemical Identifer (InChI) that uniquely identifies this molecule.
    Format: Single
    Class: String
    Programmatic Pattern: InChIKeyP

    CAS

    Chemical Abstracts Service (CAS) registry number for this molecule.
    Format: Single
    Class: String
    Programmatic Pattern: _String

    IUPAC

    International Union of Pure and Applied Chemistry (IUPAC) name for this molecule.
    Format: Single
    Class: String
    Programmatic Pattern: _String

    Species

    The source species that this protein is found in.
    Format: Single
    Class: Link
    Programmatic Pattern: _Link
    Relation: Model[Species]

    PDBIDs

    The list of Protein Data Bank IDs for any structures of this protein that have been previously reported in literature or are publically available.
    Format: Multiple
    Class: String
    Programmatic Pattern: PDBIDP

    Antibodies

    Antibodies that are known to bind to this protein.
    Format: Multiple
    Class: Link
    Programmatic Pattern: _Link

    Transcripts

    RNA templates that synthesize this protein inside of a cell.
    Format: Multiple
    Class: Link
    Programmatic Pattern: _Link

    SecondaryAntibodies

    Secondary antibody models that bind to this antibody and can be used for labeling.
    Format: Multiple
    Class: Link
    Programmatic Pattern: _Link

Inventory

    DefaultSampleModel

    Specifies the model of sample that will be used if this model is specified to be used in an experiment.
    Format: Single
    Class: Link
    Programmatic Pattern: _Link
    Relation: Model[Sample]

Physical Properties

    MolecularFormula

    Chemical formula of this molecule (e.g. H2O, NH2, etc.).
    Format: Single
    Class: String
    Programmatic Pattern: _String

    DetectionLabel

    Indicates whether this molecule (e.g. Alexa Fluor 488) can be attached to another molecule and act as a tag that can indicate the presence and amount of the other molecule.
    Format: Single
    Class: Boolean
    Programmatic Pattern: BooleanP

    AffinityLabel

    Indicates whether this molecule has high binding capacity with certain material and can be attached to another molecule (e.g. His Tag).
    Format: Single
    Class: Boolean
    Programmatic Pattern: BooleanP

    DetectionLabels

    Indicates the tags (e.g. Alexa Fluor 488) that the molecule contains, which can indicate the presence and amount of the molecule.
    Format: Multiple
    Class: Link
    Programmatic Pattern: ObjectP[Model[Molecule]]
    Relation: Model[Molecule]

    AffinityLabels

    Indicates the tags that the molecule contains (e.g. His Tag), which has high binding capacity with other materials.
    Format: Multiple
    Class: Link
    Programmatic Pattern: ObjectP[Model[Molecule]]
    Relation: Model[Molecule]

    Targets

    Target molecules (e.g. proteins or antibodies) to which this molecule binds selectively.
    Format: Multiple
    Class: Link
    Programmatic Pattern: _Link

    State

    The physical state of a pure sample of this molecule at room temperature and pressure.
    Format: Single
    Class: Expression
    Programmatic Pattern: Solid | Liquid | Gas

    Density

    The density of a pure sample of this molecule at room temperature and pressure.
    Format: Single
    Class: Real
    Unit: 1 gram per milliliter
    Programmatic Pattern: 0 Gram Hold[GreaterP[------ Milli]] Liter

    ExtinctionCoefficients

    A measure of how strongly this molecule absorbs light at a particular wavelength.
    Format: Multiple

    [Wavelength]

      Header: Wavelength
      Class: VariableUnit

    [ExtinctionCoefficient]

      Header: ExtinctionCoefficient
      Class: VariableUnit

    Fluorescent

    Indicates if this molecule can re-emit light upon excitation.
    Format: Single
    Class: Expression
    Programmatic Pattern: BooleanP

    FluorescenceExcitation Maximums

    The wavelengths corresponding to the highest peak of each Fluorescent moiety's excitation spectrum.
    Format: Multiple
    Class: Real
    Unit: 1 nanometer
    Programmatic Pattern: GreaterP[0 Nanometer]

    FluorescenceEmissionMaximums

    For each member of FluorescenceExcitationMaximums, the corresponding highest peak of the fluorescent moiety's emission spectrum.
    Format: Multiple
    Class: Real
    Unit: 1 nanometer
    Programmatic Pattern: GreaterP[0 Nanometer]

    MolecularWeight

    The molecular weight of this molecule (the mass of one mole of the molecule).
    Format: Single
    Class: Real
    Unit: 1 gram per mole
    Programmatic Pattern: 0 Gram Hold[GreaterP[------]] Mole

    ExactMass

    The most abundant mass of the molecule calculated using the natural abundance of isotopes on Earth.
    Format: Single
    Class: Real
    Unit: 1 gram per mole
    Programmatic Pattern: 0 Gram Hold[GreaterP[------]] Mole

    StructureImageFile

    An image depicting the molecule's chemical structure.
    Format: Single
    Class: Link
    Programmatic Pattern: ObjectP[Object[EmeraldCloudFile]]

    StructureFile

    A file that contains the molecule's chemical structure.
    Format: Single
    Class: Link
    Programmatic Pattern: ObjectP[Object[EmeraldCloudFile]]

    MeltingPoint

    Melting temperature of a pure sample of this molecule at atmospheric pressure.
    Format: Single
    Class: Real
    Unit: 1 degree Celsius
    Programmatic Pattern: GreaterP[0 Kelvin]

    BoilingPoint

    Temperature at which a pure sample of this molecule boils under atmospheric pressure.
    Format: Single
    Class: Real
    Unit: 1 degree Celsius
    Programmatic Pattern: GreaterP[0 Kelvin]

    VaporPressure

    Vapor pressure of a pure sample of this molecule at room temperature.
    Format: Single
    Class: Real
    Unit: 1 kilopascal
    Programmatic Pattern: GreaterEqualP[0 Kilo Pascal]

    Viscosity

    The viscosity of a pure sample of this molecule at room temperature.
    Format: Single
    Class: Real
    Unit: 1 second pascal
    Programmatic Pattern: GreaterEqualP[0 Pascal Second]

    pKa

    The logarithmic acid dissociation constants of a pure sample of this molecule at room temperature.
    Format: Multiple
    Class: Real
    Programmatic Pattern: NumericP

    NMRSolventPeak

    The known chemical shift for a given nucleus for this molecule.
    Format: Multiple

    [Nucleus]

      Header: Nucleus
      Class: String

    [ChemicalShift]

      Header: ChemicalShift
      Class: Real
      Unit: 1 part per million

    Chiral

    Indicates if this molecule is a enantiomer, that cannot be superposed on its mirror image by any combination of rotations and translations.
    Format: Single
    Class: Expression
    Programmatic Pattern: BooleanP

    Racemic

    Indicates if this molecule represents equal amounts of left- and right-handed enantiomers of a chiral molecule.
    Format: Single
    Class: Expression
    Programmatic Pattern: BooleanP

    EnantiomerForms

    If this molecule is racemic (Racemic -> True), indicates models for its left- and right-handed enantiomers.
    Format: Multiple
    Class: Link
    Programmatic Pattern: _Link
    Relation: Model[Molecule]

    RacemicForm

    If this molecule is one of the enantiomers (Chiral -> True), indicates the model for its racemic form.
    Format: Single
    Class: Link
    Programmatic Pattern: _Link
    Relation: Model[Molecule]

    EnantiomerPair

    If this molecule is one of the enantiomers (Chiral -> True), indicates the model for its non-superimposable mirror imaged molecule (stereoisomer).
    Format: Single
    Class: Link
    Programmatic Pattern: _Link
    Relation: Model[Molecule]

    pH

    The logarithmic concentration of hydrogen ions of a pure sample of this molecule at room temperature and pressure.
    Format: Single
    Class: Real
    Programmatic Pattern: RangeP[0, 14]

    Organism

    The organism in which the antibody was raised. Determines the type of secondary antibody required for labeling.
    Format: Single
    Class: Expression
    Programmatic Pattern: AntibodyOrganismP

    Isotype

    The subgroup of immunoglobulin this antibody belongs to, based on variations within the constant regions of its heavy and/or light chains.
    Format: Single
    Class: Expression
    Programmatic Pattern: AntibodyIsotypeP

    Clonality

    Specifies whether the antibody is produced by one type of cells to recognize a single epitope (monoclonal) or several types of immune cells to recognize multiple epitopes (polyclonal).
    Format: Single
    Class: Expression
    Programmatic Pattern: AntibodyClonalityP

    Epitopes

    For each member of Targets, the part of the target antigen that this antibody attaches itself to, with the sequence information of the protein segment and its binding position range.
    Format: Multiple
    Class: Expression
    Programmatic Pattern: {{_Strand, GreaterP[0], GreaterP[0]}..}

Health & Safety

    Radioactive

    Indicates if this molecule emits substantial ionizing radiation.
    Format: Single
    Class: Expression
    Programmatic Pattern: BooleanP

    Ventilated

    Indicates if a pure sample of this molecule must be handled in a ventilated enclosures.
    Format: Single
    Class: Expression
    Programmatic Pattern: BooleanP

    Flammable

    Indicates if a pure sample of this molecule is easily set aflame at room temperature and pressure.
    Format: Single
    Class: Expression
    Programmatic Pattern: BooleanP

    Acid

    Indicates if pure samples of this molecule are strong acids (pH <= 2).
    Format: Single
    Class: Expression
    Programmatic Pattern: BooleanP

    Base

    Indicates if pure samples of this molecule are strong acids (pH >= 12).
    Format: Single
    Class: Expression
    Programmatic Pattern: BooleanP

    Pyrophoric

    Indicates if pure samples of this molecule can ignite spontaneously upon exposure to air.
    Format: Single
    Class: Expression
    Programmatic Pattern: BooleanP

    WaterReactive

    Indicates if pure samples of this molecule react spontaneously upon exposure to water.
    Format: Single
    Class: Expression
    Programmatic Pattern: BooleanP

    Fuming

    Indicates if pure samples of this molecule emit fumes spontaneously when exposed to air.
    Format: Single
    Class: Expression
    Programmatic Pattern: BooleanP

    HazardousBan

    Indicates this molecule is currently banned from usage in the ECL because the facility isn't yet equiped to handle it.
    Format: Single
    Class: Expression
    Programmatic Pattern: BooleanP

    ExpirationHazard

    Indicates if pure samples of this molecule become hazardous once they are expired and must be automatically disposed of when they pass their expiration date.
    Format: Single
    Class: Boolean
    Programmatic Pattern: BooleanP

    ParticularlyHazardous Substance

    Indicates if special precautions should be taken in handling this molecule, as indicated by the MSDS classification.
    Format: Single
    Class: Expression
    Programmatic Pattern: BooleanP

    DrainDisposal

    Indicates if this molecule may be safely disposed down a standard drain.
    Format: Single
    Class: Expression
    Programmatic Pattern: BooleanP

    Pungent

    Indicates if pure samples of this molecule have a strong odor.
    Format: Single
    Class: Boolean
    Programmatic Pattern: BooleanP

    MSDSRequired

    Indicates if an MSDS is required for this molecule.
    Format: Single
    Class: Expression
    Programmatic Pattern: BooleanP

    MSDSFile

    The PDF of the MSDS (Materials Saftey Data Sheet) of this molecule.
    Format: Single
    Class: Link
    Programmatic Pattern: _Link

    NFPA

    The National Fire Protection Association (NFPA) 704 hazard diamond classification for this molecule.
    Format: Single
    Class: Expression
    Programmatic Pattern: NFPAP

    DOTHazardClass

    The Department of Transportation hazard classification for this molecule.
    Format: Single
    Class: String
    Programmatic Pattern: DOTHazardClassP

    BiosafetyLevel

    The Biosafety classification for this molecule.
    Format: Single
    Class: Expression
    Programmatic Pattern: BiosafetyLevelP

Storage Information

    LightSensitive

    Indicates if this molecule reacts or degrades in the presence of light.
    Format: Single
    Class: Expression
    Programmatic Pattern: BooleanP

Compatibility

    IncompatibleMaterials

    A list of materials that would be damaged if wetted by this molecule.
    Format: Multiple
    Class: Expression
    Programmatic Pattern: MaterialP | None

    LiquidHandlerIncompatible

    Indicates if pure samples of this molecule cannot be reliably aspirated or dispensed on an automated liquid handling robot.
    Format: Single
    Class: Expression
    Programmatic Pattern: BooleanP

    PipettingMethod

    The pipetting parameters used to manipulate pure samples of this model.
    Format: Single
    Class: Link
    Programmatic Pattern: _Link

    UltrasonicIncompatible

    Indicates if pure samples of this molecule cannot be performed via the ultrasonic distance method due to vapors interfering with the reading.
    Format: Single
    Class: Expression
    Programmatic Pattern: BooleanP

    FluorescenceLabelingTarget

    The types of molecules that cause fluorescence enhancement upon binding to this fluorophore.
    Format: Multiple
    Class: Expression
    Programmatic Pattern: FluorescenceLabelingTargetTypeP

Experimental Results

    ReferenceNMR

    Data that exemplify the expected NMR spectrum for this molecule.
    Format: Multiple
    Class: Link
    Programmatic Pattern: _Link
    Relation: Object[Data]

    ReferenceMassSpectra

    Data that exemplify the expected mass spectrometry spectrum for this molecule.
    Format: Multiple
    Class: Link
    Programmatic Pattern: _Link
    Relation: Object[Data]

    ReferenceChromatographs

    Data that exemplify expected analytical HPLC traces for this molecule.
    Format: Multiple
    Class: Link
    Programmatic Pattern: _Link
    Relation: Object[Data]

    ReferenceTLC

    Data that exemplify expected thin layer chromatography results for this molecule.
    Format: Multiple
    Class: Link
    Programmatic Pattern: _Link
    Relation: Object[Data]

Analysis & Reports

General

    AssayTypes

    Types of experiments in which this antibody is known to perform well.
    Format: Multiple
    Class: Expression
    Programmatic Pattern: AntibodyAssayCompatibilityP

    RecommendedDilution

    The dilution that is recommended for use of this antibody in a capillary electrophoresis western blot assay.
    Format: Single
    Class: Real
    Programmatic Pattern: RangeP[0, 1, Inclusive -> Right]
Last modified on Mon 26 Sep 2022 15:43:55