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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 Folding Quality Check in the RER01:29

Protein 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...
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.
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...
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...

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Related Experiment Video

Updated: Jul 14, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

firestar--prediction of functionally important residues using structural templates and alignment reliability.

Gonzalo López1, Alfonso Valencia, Michael L Tress

  • 1Structural Biology and Biocomputing Program, Spanish National Cancer Research Centre (CNIO) Melchor Fernández Almagro, 3, E-28029, Madrid, Spain. glopez@cnio.es

Nucleic Acids Research
|June 23, 2007
PubMed
Summary

Firestar predicts ligand-binding residues in protein structures by analyzing conservation and functional importance. This tool helps evaluate the biological relevance of small molecule ligands in protein data bank structures.

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Bioinformatics

Background:

  • Ligand-binding site prediction is crucial for understanding protein function.
  • Existing databases like FireDB store functionally important residues.

Purpose of the Study:

  • To present Firestar, an expert system for predicting ligand-binding residues in protein structures.
  • To provide a tool for evaluating the biological relevance of small molecule ligands in PDB structures.

Main Methods:

  • Extrapolation from the FireDB database of functionally important residues.
  • Incorporation of local conservation data for potential binding residues.
  • Querying by protein sequence or structure with access to alignments and conservation displays.

Main Results:

  • Firestar enables prediction of ligand-binding residues.
  • The system facilitates comparison of binding residue conservation across homologous proteins.
  • Biological relevance of small molecule ligands in PDB structures can be assessed.

Conclusions:

  • Firestar is a valuable tool for protein structure analysis and ligand binding site prediction.
  • The system aids in discerning conserved small molecule binding in homologous structures.
  • Firestar proved useful in CASP7 function prediction assessments.