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Related Concept Videos

Protein Organization01:24

Protein Organization

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.
Protein Organization01:13

Protein Organization

Overview
Protein Organization01:24

Protein Organization

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.
Protein and Protein Structure02:15

Protein and Protein Structure

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 can...
Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

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 form...
Protein and Protein Structures02:15

Protein and Protein Structures

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 can...

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Related Experiment Video

Updated: May 20, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Probabilistic ensembles for improved inference in protein-structure determination.

Ameet Soni1, Jude Shavlik

  • 1Department of Computer Sciences, Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53706, USA. soni@cs.wisc.edu

Journal of Bioinformatics and Computational Biology
|July 20, 2012
PubMed
Summary
This summary is machine-generated.

Automating protein structure determination using X-ray crystallography is advanced by Probabilistic Ensembles in ACMI (PEA). This new framework improves accuracy and completeness of protein models, overcoming limitations of previous methods.

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Last Updated: May 20, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction
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Published on: November 3, 2011

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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

Area of Science:

  • Structural Biology
  • Computational Biology
  • Biophysics

Background:

  • Protein X-ray crystallography is essential for structure determination but is labor-intensive.
  • Interpreting low-quality electron density maps requires significant manual effort from crystallographers.
  • Automating this process is key for high-throughput protein structure determination pipelines.

Purpose of the Study:

  • To improve the accuracy and efficiency of protein structure modeling from X-ray crystallography data.
  • To address the computational expense and error susceptibility of existing approximate inference methods.
  • To introduce a novel framework, Probabilistic Ensembles in ACMI (PEA), for enhanced protein structure estimation.

Main Methods:

  • Developed Probabilistic Ensembles in ACMI (PEA), a framework utilizing multiple independent runs of approximate inference.
  • Applied PEA to refine protein structure models generated from electron-density maps.
  • Leveraged a Markov Random Field approach within the ACMI framework to model atomic positions.

Main Results:

  • PEA demonstrated statistically significant improvements in inference accuracy.
  • The framework resulted in more complete and accurate protein structure models.
  • Showcased enhanced performance compared to previous state-of-the-art methods.

Conclusions:

  • Probabilistic Ensembles in ACMI (PEA) effectively enhances protein structure determination accuracy.
  • PEA offers a robust solution for computationally intensive inference problems in structural biology.
  • The framework provides a generalizable approach for advanced approximate inference in complex domains.