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Related Concept Videos

Protein Organization01:24

Protein Organization

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Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence....
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Protein Organization01:13

Protein Organization

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Overview
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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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Conservation of Protein Domains Over Different Proteins02:26

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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.
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Ligand Binding Sites02:40

Ligand Binding Sites

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Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
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A Protocol for Computer-Based Protein Structure and Function Prediction
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A Protocol for Computer-Based Protein Structure and Function Prediction

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Open-access data: A cornerstone for artificial intelligence approaches to protein structure prediction.

Stephen K Burley1, Helen M Berman2

  • 1Research Collaboratory for Structural Bioinformatics Protein Data Bank, Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08903, USA; Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA 92093, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA.

Structure (London, England : 1993)
|May 13, 2021
PubMed
Summary

The Protein Data Bank (PDB) archives over 175,000 macromolecular structures, enabling global research in biology and beyond. This data fuels advances in understanding protein architecture and structure prediction using AI.

Keywords:
CAMEOCAPRICASPFAIR principlesPDB50Protein Data Bankartificial intelligencede novo protein structure predictiondrug design data resourcemachine learningopen-access biodata resourceprotein structurestructural biologystructure-guided drug discovery

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Area of Science:

  • Structural Biology
  • Bioinformatics
  • Biochemistry

Background:

  • The Protein Data Bank (PDB) was founded in 1971 to publicly archive 3D structures of biological macromolecules.
  • For 50 years, the PDB has provided open access to a vast repository of experimentally determined structures.

Purpose of the Study:

  • To highlight the PDB's role as a public resource for scientific data.
  • To showcase the breadth of scientific disciplines utilizing PDB data.
  • To emphasize the PDB's contribution to advancements in structural biology and protein structure prediction.

Main Methods:

  • Archiving experimentally determined 3D structures of proteins, nucleic acids (DNA, RNA), and their complexes.
  • Providing open access to over 175,000 structural data entries.
  • Facilitating data access for millions of global users across diverse scientific fields.

Main Results:

  • The PDB currently houses more than 175,000 experimentally determined 3D structures.
  • PDB data supports research in fundamental biology, biomedicine, bioengineering, biotechnology, energy sciences, agriculture, chemistry, physics, computer science, and more.
  • The PDB archive has been instrumental in advancing the understanding of protein architecture.

Conclusions:

  • The PDB serves as a critical public resource, enabling widespread scientific inquiry and innovation.
  • The wealth of structural data in the PDB has accelerated breakthroughs, particularly in protein structure prediction through AI and machine learning.
  • Continued open access to PDB data will foster future discoveries in molecular biology and related fields.