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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 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...
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 Families02:47

Protein Families

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 locations, protein...
Protein-protein Interfaces02:04

Protein-protein Interfaces

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 polypeptide...
Protein Folding Quality Check in the RER01:29

Protein Folding Quality Check in the RER

ER is the primary site for the maturation and folding of soluble and transmembrane secretory proteins. The calnexin cycle is a specific chaperone system that folds and assesses the confirmation of N-glycosylated proteins before they can exit the ER lumen. The primary players of this quality check pipeline are the lectins, ER-resident chaperones, and a glucosyl transferase enzyme. In case the calnexin system in the lumen fails to salvage a misfolded protein, it is transported to the cytoplasm...

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Updated: Jun 19, 2026

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

ProDaMa: an open source Python library to generate protein structure datasets.

Giuliano Armano1, Andrea Manconi

  • 1Department of Electrical and Electronic Engineering, University of Cagliari, P,zza D'Armi, 09123 Cagliari, Italy. armano@diee.unica.it

BMC Research Notes
|October 6, 2009
PubMed
Summary
This summary is machine-generated.

Researchers developed ProDaMa, an open-source Python library, to streamline the creation of specialized protein datasets. This tool aids in protein analysis and the development of predictive models.

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Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames
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Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames

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

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Related Experiment Videos

Last Updated: Jun 19, 2026

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

Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames
07:38

Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames

Published on: April 11, 2019

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 bioinformatics
  • Computational biology
  • Bioinformatics

Background:

  • The disparity between known protein sequences and tertiary structures necessitates automated analysis methods.
  • Developing accurate protein analysis techniques relies heavily on the quality and relevance of training data.
  • Researchers frequently require specialized datasets tailored to specific experimental needs.

Purpose of the Study:

  • To introduce ProDaMa, an open-source Python library designed to simplify the generation of specialized protein datasets.
  • To provide a tool for retrieving, organizing, updating, analyzing, and filtering protein data.

Main Methods:

  • Implementation of ProDaMa, a Python library with classes for comprehensive protein data management.
  • Utilizing ProDaMa for dataset generation for secondary structure prediction.
  • Development of a collaborative web application for creating and sharing protein structure datasets.

Main Results:

  • ProDaMa facilitates the creation of specialized datasets crucial for tasks like secondary structure prediction.
  • A collaborative web application was developed using ProDaMa for dataset generation and sharing.
  • The ProDaMa library and associated resources are publicly accessible.

Conclusions:

  • ProDaMa effectively addresses the need for specialized protein datasets in computational biology.
  • The library supports the advancement of protein structure prediction and data sharing initiatives.
  • ProDaMa offers a valuable, freely available resource for the scientific community.