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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-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-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 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...

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Related Experiment Video

Updated: Jun 22, 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

PROTDES: CHARMM toolbox for computational protein design.

María Suárez1, Pablo Tortosa, Alfonso Jaramillo

  • 1Biochemistry Laboratory, CNRS-UMR 7654, Ecole Polytechnique, 91128, Palaiseau, France, Maria.Suarez@polytechnique.edu.

Systems and Synthetic Biology
|July 3, 2009
PubMed
Summary
This summary is machine-generated.

We developed PROTDES, an open-source software for protein design. It automatically optimizes amino acid sequences to improve protein folding free energy without pairwise approximations.

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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
  • Protein engineering
  • Biochemistry

Background:

  • Protein design is crucial for developing novel therapeutics and enzymes.
  • Current methods often rely on approximations, limiting accuracy.
  • Automating the protein design process can accelerate discovery.

Purpose of the Study:

  • To present PROTDES, an open-source software for automated protein design.
  • To enable optimization of protein folding free energy without pairwise approximations.
  • To facilitate integration of molecular dynamics in protein design workflows.

Main Methods:

  • PROTDES utilizes the CHARMM molecular modeling program.
  • An iterative heuristic optimization algorithm searches for optimal amino acids and conformations.
  • Three distinct energy functions (surface area accessibility, generalized Born, effective energy) were implemented.

Main Results:

  • PROTDES successfully automates the mutation of residue positions to optimize protein structures.
  • The software allows for the integration of molecular dynamics simulations.
  • Demonstrated flexibility by implementing diverse energy functions for protein design.

Conclusions:

  • PROTDES offers a powerful, open-source tool for computational protein design.
  • The software empowers CHARMM users to customize protein design procedures.
  • Facilitates advanced protein engineering by optimizing folding free energy.