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Ligand Binding and Linkage

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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...

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Related Experiment Video

Updated: May 4, 2026

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Published on: January 26, 2024

ALFA: automatic ligand flexibility assignment.

Javier Klett¹, Álvaro Cortés-Cabrera, Rubén Gil-Redondo

¹Unidad de Bioinformática, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Campus de Cantoblanco UAM , E-28049 Madrid, Spain.

Journal of Chemical Information and Modeling

|January 8, 2014

Summary

This summary is machine-generated.

ALFA is a fast computational tool for analyzing small molecule conformations. It accurately reproduces molecular structures and is suitable for high-throughput virtual screening and drug discovery.

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Area of Science:

Computational chemistry
Molecular modeling
Drug discovery

Background:

Understanding small molecule conformations is crucial for predicting molecular behavior.
Existing methods for conformational analysis can be computationally intensive.

Purpose of the Study:

To introduce ALFA, a novel computational tool for rapid conformational analysis of small molecules.
To assess ALFA's accuracy in reproducing known molecular structures and its suitability for high-throughput screening.

Main Methods:

ALFA utilizes a custom iterative algorithm for conformational analysis.
The tool generates a set of representative conformers for small molecules.
A graphical user interface integrated with PyMOL enhances accessibility for users.

Main Results:

ALFA demonstrates high speed, enabling integration into high-throughput virtual screening protocols.
The tool accurately reproduces crystallographic X-ray structures of bound ligands.
ALFA effectively captures the conformational diversity of small molecules in various states.

Conclusions:

ALFA is an efficient and accurate tool for small molecule conformational analysis.
Its speed and accuracy make it valuable for virtual screening and drug design.
The user-friendly interface promotes broader adoption by researchers.