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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...
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...
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...
Regulation of the Unfolded Protein Response01:31

Regulation of the Unfolded Protein Response

Inositol-requiring kinase one or IRE1 is the most conserved eukaryotic unfolded protein response (UPR) receptor. It is a type I transmembrane protein kinase receptor with a distinctive site-specific RNase activity. As the binding mechanics of the misfolded proteins with the N-terminal domain of IRE-1 are unclear, three binding models — direct, indirect, and allosteric -- are proposed for receptor activation. Nevertheless, it is known that once a misfolded protein associates with IRE1, it...
Transducer Mechanism: Enzyme-Linked Receptors01:27

Transducer Mechanism: Enzyme-Linked Receptors

Enzyme-linked receptors are cell-surface receptors acting as an enzyme or associating with an enzyme intracellularly. They make excellent drug targets. Drugs can bind to the extracellular ligand-binding domain or directly affect their enzymatic domain and alter their activity.
Major types that are helpful drug targets include:

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Related Experiment Video

Updated: Jun 2, 2026

Synthesizing Amino Acids Modified with Reactive Carbonyls in Silico to Assess Structural Effects Using Molecular Dynamics Simulations
05:57

Synthesizing Amino Acids Modified with Reactive Carbonyls in Silico to Assess Structural Effects Using Molecular Dynamics Simulations

Published on: April 26, 2024

Remote thioredoxin recognition using evolutionary conservation and structural dynamics.

Grace W Tang1, Russ B Altman

  • 1Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.

Structure (London, England : 1993)
|April 13, 2011
PubMed
Summary
This summary is machine-generated.

We developed a novel thioredoxin predictor by integrating sequence and structural data. This hybrid method (HMMDF) significantly improves remote homolog detection for oxidoreductases, aiding protein engineering and disorder research.

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Last Updated: Jun 2, 2026

Synthesizing Amino Acids Modified with Reactive Carbonyls in Silico to Assess Structural Effects Using Molecular Dynamics Simulations
05:57

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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:

  • Biochemistry and Molecular Biology
  • Bioinformatics and Computational Biology

Background:

  • Thioredoxins are oxidoreductases crucial for redox signaling and protein function.
  • Thioredoxin family proteins are implicated in various diseases and have applications in protein engineering.
  • Identifying remote thioredoxin homologs remains a challenge for existing sequence- and structure-based methods.

Purpose of the Study:

  • To develop an accurate thioredoxin predictor by integrating sequence and structural information.
  • To overcome limitations in remote homolog detection for the thioredoxin family.

Main Methods:

  • Developed a hybrid prediction method (HMMDF) combining a Hidden Markov Model (HMM) with dynamic FEATURE (DF), a molecular dynamics-enhanced structure-based recognition method.
  • Evaluated HMMDF performance against standalone HMM and DF methods.

Main Results:

  • The HMMDF method achieved high precision (0.90) and recall (0.95).
  • HMMDF outperformed standalone HMM (0.92 precision, 0.87 recall) and DF (0.82 precision, 0.97 recall) in overall performance.
  • The hybrid approach balances sensitivity and specificity, effectively resolving closely related protein families.

Conclusions:

  • The HMMDF method provides a robust and accurate approach for thioredoxin identification.
  • This predictor shows strong potential for identifying novel thioredoxins, particularly in structural genomics targets.
  • Integrated sequence-structure methods enhance the detection of remote homologs in protein families.