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Related Concept Videos

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...
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 Organization01:13

Protein Organization

Overview
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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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

PROSESS: a protein structure evaluation suite and server.

Mark Berjanskii1, Yongjie Liang, Jianjun Zhou

  • 1Department of Computing Science, University of Alberta, Canada.

Nucleic Acids Research
|May 13, 2010
PubMed
Summary
This summary is machine-generated.

PROSESS is a comprehensive web server for evaluating protein structures from X-ray, NMR, and computational methods. It integrates multiple tools to assess various quality aspects, aiding structure validation for biologists and curators.

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Last Updated: Jun 13, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction
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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

Area of Science:

  • Structural Biology
  • Biophysics
  • Computational Biology

Background:

  • Protein structure determination is crucial for understanding biological function.
  • Accurate validation of experimentally or computationally derived structures is essential.
  • Existing tools often lack comprehensiveness or the ability to handle diverse data types.

Purpose of the Study:

  • To introduce PROSESS (PROtein Structure Evaluation Suite and Server), a novel web server for comprehensive protein structure evaluation.
  • To provide a unified platform for validating structures from X-ray crystallography, NMR spectroscopy, and computational modeling.
  • To integrate diverse quality assessment metrics for both global and residue-specific analysis.

Main Methods:

  • PROSESS integrates established tools like VADAR, GeNMR, ShiftX, RCI, PREDITOR, MolProbity, Xplor-NIH, and NAMD.
  • It evaluates covalent geometry, packing, torsion angles, chemical shifts, and Nuclear Overhauser Effect (NOE) data.
  • The server analyzes X-ray, NMR, and predicted protein structures, including experimental NMR data.

Main Results:

  • PROSESS provides detailed tables, images, and graphs summarizing structure quality.
  • A red-amber-green coloring scheme highlights general and residue-specific structural problems.
  • Results are benchmarked against high-quality or high-resolution protein structures.

Conclusions:

  • PROSESS offers a unique, comprehensive solution for protein structure validation.
  • It serves as a valuable tool for structural biologists and database curators.
  • The web server facilitates the assessment and validation of newly determined protein structures.