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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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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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Conservation of Protein Domains Over Different Proteins

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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.
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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

PUDGE: a flexible, interactive server for protein structure prediction.

Raquel Norel1, Donald Petrey, Barry Honig

  • 1Department of Biochemistry and Molecular Biophysics, Howard Hughes Medical Institute, Center for Computational Biology and Bioinformatics, Columbia University, 1130 St. Nicholas Avenue, New York, NY 10032, USA. rn98@columbia.edu

Nucleic Acids Research
|June 8, 2010
PubMed
Summary
This summary is machine-generated.

Pudge is a protein structure prediction server that integrates functional information. It offers a flexible, five-stage modeling process with visualization tools for tailored protein modeling.

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Last Updated: Jun 12, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction
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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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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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Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
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Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Published on: January 26, 2024

Area of Science:

  • * Computational Biology
  • * Structural Bioinformatics
  • * Protein Modeling

Background:

  • * Protein structure prediction is complex, requiring integration of diverse information and tools.
  • * Functional information is crucial for guiding protein modeling but often overlooked in pipelines.
  • * Existing modeling pipelines lack flexibility and integration of functional data.

Purpose of the Study:

  • * To introduce Pudge, a flexible, interactive protein structure prediction server.
  • * To address the need for integrating functional information into protein modeling workflows.
  • * To provide a tailored modeling strategy adaptable to specific protein structure prediction problems.

Main Methods:

  • * Pudge divides protein modeling into five distinct stages: template selection, alignment, model building, refinement, and evaluation.
  • * The server provides interactive tools for visualizing, analyzing, and comparing results at each stage.
  • * It facilitates a flexible modeling strategy by allowing users to tailor the process.

Main Results:

  • * Pudge enables a more adaptable and user-driven approach to protein homology modeling.
  • * The integration of functional information aids in guiding the modeling process effectively.
  • * The five-stage structure allows for detailed analysis and refinement at each step.

Conclusions:

  • * Pudge offers a flexible and interactive solution for protein structure prediction.
  • * The server's design supports the integration of functional information for improved modeling accuracy.
  • * Pudge provides a customizable platform for addressing diverse protein modeling challenges.