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Related Concept Videos

Ligand Binding Sites02:40

Ligand Binding Sites

Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
Ligand Binding Sites02:40

Ligand Binding Sites

Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence the...
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence 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...
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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Related Experiment Video

Updated: Jun 19, 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

Secbase: database module to retrieve secondary structure elements with ligand binding motifs.

Oliver Koch1, Jason Cole, Peter Block

  • 1Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, D-35032 Marburg, Germany.

Journal of Chemical Information and Modeling
|October 8, 2009
PubMed
Summary
This summary is machine-generated.

Secbase enhances protein structure retrieval by integrating secondary structure data. This novel module offers new insights into how protein elements like alpha-helices and beta-sheets bind ligands.

More Related Videos

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

Related Experiment Videos

Last Updated: Jun 19, 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

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:

  • Structural Biology
  • Bioinformatics
  • Computational Chemistry

Background:

  • Relibase is a protein structure database.
  • Secondary structure elements are crucial for protein function.
  • Efficient retrieval of secondary structure information is needed.

Purpose of the Study:

  • Introduce Secbase, a novel extension module for Relibase.
  • Integrate secondary structure element information into Relibase retrieval.
  • Analyze the role of secondary structures in ligand binding.

Main Methods:

  • Utilized PDB data for alpha-helices and beta-sheets.
  • Developed a uniform classification for turn families.
  • Implemented algorithms for geometric analysis of helices and beta-strands.
  • Extended Relibase user interface and query language (Reliscript).

Main Results:

  • Secbase provides enhanced retrieval of secondary structure data.
  • Identified specific binding motifs involving alpha-helix N-termini and water molecules.
  • Demonstrated the role of helix turn structure in stabilizing charged ligands.
  • Found distinct preferences for secondary structures in recognizing endogenous ligands like cofactors.

Conclusions:

  • Secbase offers powerful tools for analyzing protein secondary structures and their interactions.
  • Secondary structure elements play a significant role in ligand recognition and binding specificity.
  • The study provides novel insights into molecular recognition mechanisms in proteins.