Related Experiment Video
Updated: Jun 27, 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
PDBalert: automatic, recurrent remote homology tracking and protein structure prediction
Vatsal Agarwal1, Michael Remmert, Andreas Biegert
1Department of Biotechnology, Indian Institute of Technology, Roorkee 247667, India. agvatubt@iitr.ernet.in
BMC Structural Biology
|November 26, 2008
Summary
PDBalert is a new system that automatically alerts researchers when new protein structures are available in the Protein Data Bank (PDB). This helps in timely 3D structure and function prediction using remote homology detection.
Area of Science:
- Biochemistry
- Structural Biology
- Bioinformatics
Background:
- Remote homology detection methods have advanced, enabling 3D model generation even with low sequence identity.
- Current methods require users to repeatedly search the Protein Data Bank (PDB) for new homologous structures.
- This manual process can delay the utilization of newly available protein data.
Purpose of the Study:
- To develop an automated system for monitoring the PDB for new protein structures.
- To provide timely alerts to researchers regarding newly released homologous structures.
- To facilitate the prediction of 3D protein structures and functions.
Main Methods:
- Implemented PDBalert, a web-based system for automatic structure monitoring.
- Utilized HHpred software, a sensitive remote homology detection server based on Hidden Markov Models.
- Integrated email alerts containing links to search results and automated 3D homology models.
Main Results:
- PDBalert sends email notifications upon the release of new homologous structures in the PDB.
- Alerts include direct links to homology search results and generated 3D models.
- The system leverages advanced remote homology detection software for accuracy.
Conclusions:
- PDBalert significantly accelerates information flow from the PDB.
- Researchers can benefit from timely access to new protein structures for their studies.
- The system aids in predicting 3D structure and function of proteins of interest.
Related Concept Videos
02:15Protein 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...
A protein's shape is critical to its function. For example, an enzyme can...
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...
02:47Protein Families
Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism. Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members. If these new proteins contain similar amino acids in key locations, protein...
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...
02:15Protein 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...
A protein's shape is critical to its function. For example, an enzyme can...
01:24Protein 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.
The primary structure of a protein is its amino acid sequence.