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Related Concept Videos

Protein Folding01:25

Protein Folding

Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...
Protein Folding01:22

Protein Folding

Overview
Protein Folding01:22

Protein Folding

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Molecular Chaperones and Protein Folding03:00

Molecular Chaperones and Protein Folding

The native conformation of a protein is formed by interactions between the side chains of its constituent amino acids. When the amino acids cannot form these interactions, the protein cannot fold by itself and needs chaperones. Notably, chaperones do not relay any additional information required for the folding of polypeptides; the native conformation of a protein is determined solely by its amino acid sequence. Chaperones catalyze protein folding without being a part of the folded protein.
The...
Molecular Chaperones and Protein Folding03:00

Molecular Chaperones and Protein Folding

The native conformation of a protein is formed by interactions between the side chains of its constituent amino acids. When the amino acids cannot form these interactions, the protein cannot fold by itself and needs chaperones. Notably, chaperones do not relay any additional information required for the folding of polypeptides; the native conformation of a protein is determined solely by its amino acid sequence. Chaperones catalyze protein folding without being a part of the folded protein.
The...
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.

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Updated: Jun 23, 2026

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

Computational protein design as a tool for fold recognition.

Marcel Schmidt am Busch1, David Mignon, Thomas Simonson

  • 1Laboratoire de Biochimie (CNRS UMR7654), Department of Biology, Ecole Polytechnique, 91128 Palaiseau, France.

Proteins
|May 2, 2009
PubMed
Summary

Computational protein design can identify novel sequences for fold recognition and homology searching. Designed SH3 and SH2 protein sequences show native-like characteristics and can detect natural protein families.

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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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A Protocol for Computer-Based Protein Structure and Function Prediction
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A Protocol for Computer-Based Protein Structure and Function Prediction

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

Area of Science:

  • Computational biology
  • Protein engineering
  • Bioinformatics

Background:

  • Protein sequence design is crucial for understanding protein function and evolution.
  • Computational methods offer a powerful approach to designing novel protein sequences.
  • The ability to computationally design proteins for fold recognition and homology searching remains an active area of research.

Purpose of the Study:

  • To investigate the potential of computationally designed protein sequences for fold recognition and homology searching.
  • To redesign existing SH3 and SH2 protein families using computational methods.
  • To assess the native-like character and detectability of designed protein sequences using standard bioinformatics tools.

Main Methods:

  • Utilized experimental backbone coordinates as fixed templates.
  • Employed a molecular mechanics model to compute pairwise interaction energies.
  • Used the Proteins@Home volunteer computing platform for energy calculations.
  • Applied a heuristic algorithm to scan sequence and conformational space for optimal solutions.
  • Generated hundreds of thousands of sequences per template.

Main Results:

  • Designed sequences exhibited moderate similarity to natural homologues.
  • 61% (SH3) and 52% (SH2) of low-energy designed sequences were recognized by the Conserved Domain Database.
  • 81% (SH3) and 84% (SH2) were recognized by the SUPERFAMILY Hidden-Markov Model library.
  • Position-specific scoring matrices (PSSMs) from designed sequences effectively detected natural homologues.
  • Resetting substrate-binding residues improved detection rates for SH3 domains to 77%.

Conclusions:

  • Computationally designed protein sequences can mimic native-like structures and functions.
  • Designed sequences and their derived PSSMs are valuable for homology searching.
  • The computational design approach shows promise for discovering new protein families and understanding protein evolution.
  • Further refinements, particularly accounting for substrate-binding interactions, can enhance design accuracy.