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Related Concept Videos

Archival Research01:40

Archival Research

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Some researchers gain access to large amounts of data without interacting with a single research participant. Instead, they use existing records to answer various research questions. This type of research approach is known as archival research. Archival research relies on looking at past records or data sets to look for interesting patterns or relationships. For example, a researcher might access the academic records of all individuals who enrolled in college within the past ten years and...
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Growth Models with Integration: Problem Solving01:27

Growth Models with Integration: Problem Solving

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In population modeling, integration provides a systematic way to determine accumulated quantities from known rates of change. One such application arises in ecology, where the total weight of a fish population in a body of water is referred to as its biomass. When the rate of growth of this biomass is known as a function of time, calculus can be used to determine the total biomass at a future date.Growth Rate and Biomass FunctionLet the growth rate of the fish population be represented by a...
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Structure of Benzene: Kekulé Model01:07

Structure of Benzene: Kekulé Model

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In 1865, August Kekule suggested the structure of benzene according to the structural theory of organic chemistry based on the three assertions—formula of benzene is C6H6, all the hydrogens of benzene are equivalent, and each carbon must have four bonds due to its tetravalency.
He proposed that benzene has a cyclic structure of six carbon atoms attached to one hydrogen atom each, with three alternating pi bonds.
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Structure of Benzene: Molecular Orbital Model01:18

Structure of Benzene: Molecular Orbital Model

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According to the molecular orbital (MO) model, benzene has a planar structure with a regular hexagon of six sp2 hybridized carbons. As shown in Figure 1, each carbon is bonded to three other atoms with C–C–C and H–C–C bond angles of 120°. The C–H bond length is 109 pm, and the C–C bond length is 139 pm which is midway between the single bond length of sp3 hybridized carbons (154 pm) and sp2 hybridized carbons (133 pm).
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Definite Integral01:29

Definite Integral

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Consider a real-valued function defined on a closed interval. One of the fundamental objectives in calculus is to determine the area under the graph of such a function. When an exact computation is not readily available, this area can be estimated by dividing the interval into a finite number of equal subintervals. Each subinterval corresponds to a rectangle whose width is the length of the subinterval and whose height is determined by the value of the function at a selected point within that...
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Indefinite Integrals01:25

Indefinite Integrals

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The water inflow rate into a storage tank is not constant but increases over time. Initially, the pump delivers water at a rate of 5 L/min. However, the inflow rate increases by 2 L/min for each additional minute due to rising pressure or system adjustments. This scenario can be described mathematically by a linear function:It is necessary to integrate the inflow rate function to measure the total volume of water added to the tank over time. The total water volume V(t) is obtained by performing...
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Archiving and disseminating integrative structure models.

Brinda Vallat1, Benjamin Webb2, John Westbrook1,3

  • 1Institute for Quantitative Biomedicine, Piscataway, USA.

Journal of Biomolecular NMR
|July 7, 2019
PubMed
Summary
This summary is machine-generated.

Integrative modeling combines diverse data for enhanced structural biology. Archiving these models, experimental data, and protocols ensures reproducibility and validation, advancing structural biology research.

Keywords:
DepositionHybrid modelingIntegrative modelingModel validationPDBmmCIF dictionary

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Area of Science:

  • Structural Biology
  • Computational Biology
  • Biophysics

Background:

  • Individual structure characterization methods have limitations in applicability, accuracy, and precision.
  • Integrative modeling offers a solution by combining information from multiple experimental sources and prior models.
  • The open-source Integrative Modeling Platform (IMP) facilitates computational aspects of integrative modeling.

Purpose of the Study:

  • To establish standards and infrastructure for archiving and disseminating integrative structural models.
  • To ensure reproducibility and validation of integrative structural models.
  • To extend existing data representation formats for integrative structural biology.

Main Methods:

  • Development of the Integrative/Hybrid Methods Task Force recommendations.
  • Extension of the PDBx/mmCIF data representation to create the IHM-dictionary for integrative models.
  • Creation of the PDB-Dev prototype archiving system and a supporting Python library.

Main Results:

  • The IHM-dictionary enables flexible representation of integrative models, including coarse-graining and multi-state models.
  • PDB-Dev provides a prototype system for archiving integrative structural models and associated data.
  • A Python library simplifies handling of integrative models in PDBx/mmCIF format.

Conclusions:

  • Public archiving of integrative structures, experimental data, and protocols is crucial for maximizing impact.
  • Standardized data representation and archiving systems are essential for the structural biology community.
  • Validation of integrative structures during publication and deposition is a key recommendation.