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Related Concept Videos

Protein Families02:47

Protein Families

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Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism.   Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members.   If these new proteins contain similar amino acids in key...
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Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

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Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
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Rab Proteins01:14

Rab Proteins

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Rab proteins constitute the largest family of monomeric GTPases, of which 70 members are present in humans. Rab proteins and their effectors regulate consecutive stages of vesicle transport such as vesicle transport, docking, and fusion to the correct recipient membrane.
Rab proteins switch between a cytosolic, GDP-bound inactive state and a membrane-anchored, GTP-bound active state. By themselves, Rabs show slow rates of GDP/GTP exchange and GTP hydrolysis. Thus, Rab proteins are considered...
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Protein and Protein Structure02:15

Protein and Protein Structure

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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.
A protein's shape is critical to its function. For example, an enzyme...
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Protein-protein Interfaces02:04

Protein-protein Interfaces

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Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...
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Ribosome Profiling02:24

Ribosome Profiling

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Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
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rcsb-api: Python Toolkit for Streamlining Access to RCSB Protein Data Bank APIs.

Dennis W Piehl1, Brinda Vallat2, Ivana Truong1

  • 1Research Collaboratory for Structural Bioinformatics Protein Data Bank and the Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.

Journal of Molecular Biology
|February 2, 2025
PubMed
Summary
This summary is machine-generated.

A new Python package, rcsb-api, simplifies programmatic access to the Protein Data Bank's vast archive of 3D macromolecular structures. This tool accelerates research in structural biology and drug discovery by streamlining data retrieval and analysis.

Keywords:
FAIR principlesRCSB Protein Data BankRCSB.orgbioinformaticsstructural biology

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Area of Science:

  • Structural Biology
  • Bioinformatics
  • Computational Biology

Background:

  • The Protein Data Bank (PDB) is the primary global archive for experimentally determined 3D macromolecular structures.
  • RCSB.org provides a web portal for accessing PDB data and computed structure models.
  • Programmatic access to the extensive PDB data can be challenging for researchers.

Purpose of the Study:

  • To develop a user-friendly Python software package for accessing RCSB PDB APIs.
  • To streamline the process of searching, retrieving, and analyzing 3D biostructure data.
  • To accelerate research across various biological and biomedical disciplines.

Main Methods:

  • Development of the rcsb-api Python package.
  • Leveraging existing RCSB PDB Application Programming Interfaces (APIs).
  • Publication on GitHub and PyPI for accessibility.

Main Results:

  • The rcsb-api package provides an efficient interface for PDB data.
  • Facilitates seamless integration and analysis of structural biology data.
  • Enhances programmatic access to over 230,000 experimentally determined structures.

Conclusions:

  • The rcsb-api Python package simplifies access to the PDB, accelerating research.
  • This tool supports researchers in structural biology, drug discovery, and bioinformatics.
  • Wider adoption is expected to advance fundamental and applied biological sciences.