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Related Concept Videos

Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

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.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
Conservation of Protein Domains02:26

Conservation of Protein Domains

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.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
Structural Protein Function01:56

Structural Protein Function

Structural proteins are a category of proteins responsible for functions ranging from cell shape and movement to providing support to major structures such as bones, cartilage, hair, and muscles. This group includes proteins such as collagen, actin, myosin, and keratin.
Collagen, the most abundant protein in mammals, is found throughout the body. In connective tissue, such as skin, ligaments, and tendons, it provides tensile strength and elasticity.  In bones and teeth, it mineralizes to form...
Structural Protein Function01:56

Structural Protein Function

Structural proteins are a category of proteins responsible for functions ranging from cell shape and movement to providing support to major structures such as bones, cartilage, hair, and muscles. This group includes proteins such as collagen, actin, myosin, and keratin.
Collagen, the most abundant protein in mammals, is found throughout the body. In connective tissue, such as skin, ligaments, and tendons, it provides tensile strength and elasticity.  In bones and teeth, it mineralizes to form...
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...

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Related Experiment Video

Updated: May 11, 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

EvoDesign: De novo protein design based on structural and evolutionary profiles.

Pralay Mitra1, David Shultis, Yang Zhang

  • 1Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109 USA.

Nucleic Acids Research
|May 15, 2013
PubMed
Summary

EvoDesign improves protein sequence design by integrating evolutionary profiles and neural network predictions. This method enhances protein foldability and stability compared to traditional physics-based approaches.

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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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Last Updated: May 11, 2026

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
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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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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

Area of Science:

  • Computational biology
  • Protein engineering
  • Bioinformatics

Background:

  • De novo protein design seeks novel sequences with specific structures and functions.
  • Current methods often use physics-based force fields, limited by inaccurate atomic interaction descriptions.
  • Inaccurate force fields hinder the accurate prediction of protein folding and stability.

Purpose of the Study:

  • To develop an advanced computational tool for designing optimal protein sequences.
  • To improve the assessment of protein foldability and design quality using sequence and structure features.
  • To overcome limitations of existing physics-based protein design methods.

Main Methods:

  • Developed the EvoDesign web server for protein sequence design.
  • Employed an evolution-profile-based Monte Carlo search using homologous protein families from the Protein Data Bank.
  • Integrated local structure features (secondary structure, torsion angle, solvation) predicted by neural networks.

Main Results:

  • EvoDesign designs optimal protein sequences for given scaffolds.
  • The server assesses foldability and design quality using multiple sequence and structure-based features.
  • Designed sequences demonstrated enhanced foldability and structural stability in large-scale experiments.

Conclusions:

  • EvoDesign offers a novel approach to protein design, outperforming traditional physics-based methods.
  • The integration of evolutionary information and neural network predictions improves design accuracy.
  • The EvoDesign server provides a valuable resource for protein engineering and computational biology research.