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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...
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...
Predicting Molecular Geometry02:27

Predicting Molecular Geometry

VSEPR Theory for Determination of Electron Pair Geometries
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...
Noncovalent Attractions in Biomolecules02:35

Noncovalent Attractions in Biomolecules

Noncovalent attractions are associations within and between molecules that influence the shape and structural stability of complexes. These interactions differ from covalent bonding in that they do not involve sharing of electrons.
Four types of noncovalent interactions are hydrogen bonds, van der Waals forces, ionic bonds, and hydrophobic interactions.
Hydrogen bonding results from the electrostatic attraction of a hydrogen atom covalently bonded to a strong-electronegative atom like oxygen,...
The Equilibrium Binding Constant and Binding Strength02:18

The Equilibrium Binding Constant and Binding Strength

The equilibrium binding constant (Kb) quantifies the strength of a protein-ligand interaction. Kb can be calculated as follows when the reaction is at equilibrium:

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Related Experiment Video

Updated: Jun 22, 2026

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

Prediction of sub-cavity binding preferences using an adaptive physicochemical structure representation.

Izhar Wallach1, Ryan H Lilien

  • 1Department of Computer Science, Donnelly Centre for Cellular and Biomolecular Research and Banting and Best, University of Toronto, Toronto, Ontario, Canada. izharw@cs.toronto.edu

Bioinformatics (Oxford, England)
|May 30, 2009
PubMed
Summary

A new algorithm predicts protein binding profiles by analyzing sub-cavities, improving drug discovery for novel proteins lacking structural similarity to known targets.

More Related Videos

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

Related Experiment Videos

Last Updated: Jun 22, 2026

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

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

Area of Science:

  • Computational biology
  • Structural bioinformatics
  • Drug discovery

Background:

  • Predicting protein binding profiles is crucial for drug discovery and function prediction.
  • Current methods fail for novel proteins lacking structural similarity to known ones.
  • Existing algorithms rely on templates or whole active site comparisons.

Purpose of the Study:

  • To develop a novel algorithm for predicting binding profiles of arbitrary proteins.
  • To overcome limitations of existing methods in characterizing novel protein active sites.
  • To leverage sub-cavity analysis for improved binding inference.

Main Methods:

  • Characterizing binding preferences of sub-cavities within protein active sites.
  • Utilizing a large dataset of known protein-ligand complexes.
  • Employing a unique approach for sub-cavity representation, parametrization, and comparison based on local structural similarity.

Main Results:

  • The algorithm accurately clusters similar sub-cavities.
  • Binding patterns are predicted across diverse protein-ligand complexes.
  • Successful generation of binding profiles for high-profile drug targets consistent with known inhibitors.

Conclusions:

  • The developed algorithm shows promise for structure-based drug discovery.
  • It can aid in lead optimization by predicting binding profiles for novel targets.
  • The method expands the applicability of binding inference to proteins without significant structural similarity to known systems.