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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...
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...
Assembly of Signaling Complexes01:30

Assembly of Signaling Complexes

Multiprotein signaling complexes are formed in a dynamic process involving protein-protein interactions at the cytoplasmic domain of transmembrane receptors or enzymatic and non-enzymatic proteins associated with the receptor. These complexes ensure the activation and propagation of intracellular signals that regulate cell functions.
Interaction domains in cell signaling
Interaction domains recognize exposed features of their binding partners containing post-translationally modified sequences,...

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Related Experiment Video

Updated: Jul 17, 2026

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
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Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

[Receptor-ligand docking simulation for membrane proteins].

Takatsugu Hirokawa1

  • 1Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, AIST Tokyo Waterfront Bio-IT Research Building, Koto-ku, Tokyo, Japan. t-hirokawa@aist.go.jp

Yakugaku Zasshi : Journal of the Pharmaceutical Society of Japan
|January 5, 2007
PubMed
Summary

A new computational method, comparative ligand-binding analysis (CoLBA), predicts how ligands bind to G-protein-coupled receptors (GPCRs). This technique enhances drug discovery by improving virtual screening accuracy for these important drug targets.

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Area of Science:

  • Computational chemistry and structural biology.
  • Drug discovery and medicinal chemistry.

Context:

  • G-protein-coupled receptors (GPCRs) are crucial drug targets, but experimental structural data for ligand-bound states are scarce.
  • Existing computational methods for predicting ligand-receptor interactions in GPCRs often require manual expert input for ligand conformation.
  • Difficulties in GPCR crystallization limit the application of traditional structure-based drug design.

Purpose:

  • To develop an automated and accurate computational method for predicting ligand-receptor binding in GPCRs.
  • To overcome limitations in experimental structural data and manual prediction steps in GPCR drug discovery.
  • To introduce comparative ligand-binding analysis (CoLBA) for enhanced virtual screening and molecular modeling.

Summary:

  • Developed comparative ligand-binding analysis (CoLBA), a molecular modeling technique for predicting ligand-receptor binding.
  • CoLBA integrates interaction energy with interaction profile similarity for more robust predictions.
  • Successfully applied CoLBA to predict ligand binding in GPCRs and validated through mutagenesis and virtual screening simulations.

Impact:

  • CoLBA facilitates intuitive and flexible virtual screening, even with low-resolution or theoretical protein models.
  • The method enhances the enrichment rate of active ligands in virtual screening simulations.
  • CoLBA offers a scalable approach for large-scale modeling of ligand-receptor complexes and virtual screening of GPCRs, accelerating drug discovery.