Related Experiment Video
Updated: Jun 23, 2026
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
pGenTHREADER and pDomTHREADER: new methods for improved protein fold recognition and superfamily discrimination
Anna Lobley1, Michael I Sadowski, David T Jones
1Department of Computer Science, University College London, UK.
Bioinformatics (Oxford, England)
|May 12, 2009
Summary
GenTHREADER and pDomTHREADER improve protein structure prediction and homology detection. These bioinformatics tools enhance template detection and superfamily discrimination, benefiting downstream applications.
Area of Science:
- Bioinformatics
- Computational Biology
- Structural Biology
Background:
- Accurate protein structure modeling and homologous relationship identification are crucial for unannotated protein sequences.
- Enhancing sensitivity and selectivity in these tasks offers significant downstream benefits for various bioinformatics applications.
Purpose of the Study:
- To present an improved GenTHREADER method for large-scale protein structure prediction.
- To introduce pDomTHREADER for enhanced discrimination of protein superfamilies.
Main Methods:
- GenTHREADER utilizes profile-profile alignments, secondary-structure specific gap penalties, and solvation potentials, optimized via a support vector machine (SVM) regression model.
- pDomTHREADER integrates both sequence and structural data for remote homology detection.
Main Results:
- The latest GenTHREADER implementation shows improved template detection and sequence-structure alignment accuracy compared to other methods.
- pDomTHREADER demonstrates superior sensitivity and selectivity in superfamily discrimination over existing standard methods.
Conclusions:
- The developed GenTHREADER and pDomTHREADER methods represent significant advancements in protein structure prediction and homology detection.
- These tools provide more accurate and sensitive solutions for fundamental bioinformatics challenges.
Related Concept Videos
02:26Conservation 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...
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
01:22Protein Folding
Overview
01:22Protein Folding
Overview
01:25Protein 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 Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...
02:26Conservation 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...
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
01:29Protein Folding Quality Check in the RER
ER is the primary site for the maturation and folding of soluble and transmembrane secretory proteins. The calnexin cycle is a specific chaperone system that folds and assesses the confirmation of N-glycosylated proteins before they can exit the ER lumen. The primary players of this quality check pipeline are the lectins, ER-resident chaperones, and a glucosyl transferase enzyme. In case the calnexin system in the lumen fails to salvage a misfolded protein, it is transported to the cytoplasm...