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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...
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...
Protein-protein Interfaces02:04

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...
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.
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...

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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

Recognizing protein-ligand binding sites by global structural alignment and local geometry refinement.

Ambrish Roy1, Yang Zhang

  • 1Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109-2218, USA.

Structure (London, England : 1993)
|May 8, 2012
PubMed
Summary
This summary is machine-generated.

We developed COFACTOR, a novel computational method to identify protein-ligand binding sites using low-resolution models. This approach accurately predicts functional sites, aiding in understanding protein interactions and drug discovery.

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Last Updated: May 22, 2026

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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:

  • Computational Biology
  • Structural Biology
  • Bioinformatics

Background:

  • Protein functions are mediated by interactions with other molecules, but structural details of these interactions are often unknown.
  • Understanding protein-ligand interactions is crucial for deciphering biological processes and developing therapeutics.

Purpose of the Study:

  • To present COFACTOR, a comparative approach for recognizing functional protein-ligand interaction sites.
  • To evaluate COFACTOR's performance using low-resolution protein structural models.

Main Methods:

  • Utilized a global-to-local sequence and structural comparison algorithm.
  • Applied COFACTOR to 501 proteins with 582 natural and drug-like ligands, using I-TASSER structure predictions.
  • Assessed binding-site prediction accuracy and compared performance against other methods like FINDSITE and ConCavity.

Main Results:

  • COFACTOR successfully identified ligand-binding pocket locations for 65% of apo receptors with an average distance error of 2 Å.
  • Achieved 46% higher average precision in binding-residue assignments compared to FINDSITE and ConCavity.
  • In CASP9, COFACTOR demonstrated superior binding-site prediction precision (72%) and Matthews correlation coefficient (0.69) on blind test proteins.

Conclusions:

  • COFACTOR is a powerful structure-based method for predicting protein-ligand interactions.
  • The approach is applicable for genome-wide structural and functional annotations.
  • Demonstrates the utility of computational methods in advancing our understanding of molecular interactions.