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A schema is a mental framework that helps individuals organize and interpret information. Schemata, formed from previous experiences, influence how we process new information: how we encode it, the inferences we make, and how we retrieve it. For instance, a schema for what a typical classroom looks like might include desks, a teacher's desk, a whiteboard, and students in such an environment. This expectation helps us quickly understand and navigate new classrooms without needing to analyze...
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New system for archiving integrative structures.

Brinda Vallat1, Benjamin Webb2, Maryam Fayazi1

  • 1RCSB PDB, Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA.

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|December 6, 2021
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Summary
This summary is machine-generated.

A new system, PDB-Dev, archives and shares integrative biological structures. This platform ensures data is findable, accessible, interoperable, and reusable for researchers worldwide.

Keywords:
IHM-dictionaryPDB-DevPDBx/mmCIFdata standardsintegrative modeling

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Area of Science:

  • Structural biology
  • Biochemistry
  • Computational biology

Background:

  • Complex biological assemblies are crucial for understanding cellular functions.
  • Integrative approaches, combining multiple experimental methods, are increasingly used to determine their structures.
  • Publicly archiving and sharing these structures is essential for scientific progress.

Purpose of the Study:

  • To introduce PDB-Dev, a dedicated system for archiving and disseminating integrative structures.
  • To detail the data standards, software tools, and infrastructure supporting PDB-Dev.
  • To ensure adherence to FAIR principles for enhanced data accessibility and reusability.

Main Methods:

  • Development of a standalone archiving system (PDB-Dev).
  • Implementation of data standards and software tools for data collection, processing, and archiving.
  • Adoption of FAIR (Findable, Accessible, Interoperable, Reusable) principles.

Main Results:

  • PDB-Dev is established as a central repository for integrative structures.
  • The system's infrastructure supports efficient data management.
  • Data standards and tools facilitate the archiving process.

Conclusions:

  • PDB-Dev provides a crucial resource for the structural biology community.
  • The system promotes open science by making integrative structure data freely accessible.
  • Adherence to FAIR principles enhances the value and impact of archived structural data.