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Related Concept Videos

Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses 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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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...

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Related Experiment Video

Updated: May 12, 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

Published on: July 8, 2025

Capturing protein sequence-structure specificity using computational sequence design.

Paul Mach1, Patrice Koehl

  • 1Department of Applied Mathematics, Genome Center, University of California, Davis, 95616, California.

Proteins
|April 24, 2013
PubMed
Summary
This summary is machine-generated.

Computational protein design generates evolutionary information for protein fold recognition, improving accuracy for small protein families. This method accurately classifies protein structures even with limited native sequence data.

Keywords:
computational protein sequence designhidden Markov modelsprotein fold recognitionsequence threading

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Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
06:50

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 engineering

Background:

  • Protein fold recognition accuracy improves with evolutionary history models.
  • Limited evolutionary data hinders recognition for small protein families.

Purpose of the Study:

  • To recreate evolutionary information using computational protein design.
  • To improve protein fold recognition for protein families with sparse sequence data.

Main Methods:

  • Utilized a database of 1747 protein templates.
  • Employed computational design with fixed backbones and threaded sequences.
  • Scored models using a semi-empirical physical potential.
  • Generated hidden Markov model-based profiles from designed sequences.

Main Results:

  • Native sequences were correctly recognized (>90%) against designed profiles.
  • Homologous sequences showed lower recognition (35%) but correct structural classification (>88%).

Conclusions:

  • Computational protein design can substitute for missing evolutionary data.
  • This approach enhances protein fold recognition and structural classification for underrepresented families.