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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 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 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 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...
Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...
Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...

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Related Experiment Video

Updated: Jun 30, 2026

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
05:08

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

TESE: generating specific protein structure test set ensembles.

Francesco Sirocco1, Silvio C E Tosatto

  • 1Department of Biology, University of Padova, Viale G. Colombo 3, 35131 Padova, Italy.

Bioinformatics (Oxford, England)
|September 18, 2008
PubMed
Summary
This summary is machine-generated.

The Test Set (TESE) server generates custom protein sequence and structure datasets for method benchmarking and research needs. It allows users to select specific protein subsets based on structural and quality criteria, aiding in data analysis and dataset expansion.

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Last Updated: Jun 30, 2026

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
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Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

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16:41

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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:

  • * Bioinformatics
  • * Structural Biology
  • * Computational Biology

Background:

  • * Existing protein databases lack tailored subsets for specific research applications.
  • * Generating custom datasets for benchmarking and specialized studies is often challenging and time-consuming.

Purpose of the Study:

  • * To introduce the Test Set (TESE) web server for creating customized protein sequence and structure datasets.
  • * To provide a flexible tool for researchers to generate test sets for method benchmarking, specialized needs, and dataset extension.

Main Methods:

  • * Utilizes the CATH structure classification to manage structural and sequence redundancy.
  • * Allows interactive selection of protein subsets based on various structural quality parameters (e.g., resolution, secondary structure content, residue count).
  • * Supports the generation of multiple subsets for cross-validation purposes.

Main Results:

  • * TESE enables the creation of highly specific protein subsets, such as "all X-ray structures of alpha-helical repeat proteins with >120 residues and resolution <2.0 A."
  • * The server outputs data in standard formats: FASTA for sequences, PDB for structures, and an HTML index with protein images.
  • * Provides a user-friendly interface for accessing and manipulating protein structural and sequence data.

Conclusions:

  • * TESE offers a valuable resource for the bioinformatics and structural biology communities.
  • * The server facilitates reproducible research by enabling the generation of well-defined and reproducible test sets.
  • * TESE enhances the usability of protein structure databases for diverse computational biology applications.