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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...
Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...
Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...
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...

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Related Experiment Video

Updated: Jun 20, 2026

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
08:49

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

Published on: June 20, 2025

The flexible pocketome engine for structural chemogenomics.

Ruben Abagyan1, Irina Kufareva

  • 1Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA.

Methods in Molecular Biology (Clifton, N.J.)
|September 4, 2009
PubMed
Summary
This summary is machine-generated.

This study introduces a novel structural genomics engine for predicting small molecule interactions with proteins. This approach accelerates the discovery of new therapeutics by analyzing protein binding sites and chemical scaffolds.

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Achieving Efficient Fragment Screening at XChem Facility at Diamond Light Source
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Achieving Efficient Fragment Screening at XChem Facility at Diamond Light Source

Published on: May 29, 2021

Related Experiment Videos

Last Updated: Jun 20, 2026

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
08:49

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

Published on: June 20, 2025

Achieving Efficient Fragment Screening at XChem Facility at Diamond Light Source
08:35

Achieving Efficient Fragment Screening at XChem Facility at Diamond Light Source

Published on: May 29, 2021

Area of Science:

  • Computational biology
  • Structural biology
  • Drug discovery

Background:

  • Small molecules interact with biological macromolecules through flexible pockets to produce biological effects.
  • Advancements in structural databases, genomic data, and 3D modeling techniques enable comprehensive mapping of small molecule-biopolymer interactions.

Purpose of the Study:

  • To develop a comprehensive structural genomics engine for predicting small molecule-protein interactions.
  • To enable the prediction of binding poses and activities for novel protein binding sites and chemical scaffolds.

Main Methods:

  • Utilizing multiple protein pocket conformations (experimentally determined or modeled).
  • Employing efficient ensemble docking algorithms.
  • Integrating structural data with advanced docking, scoring, and profiling methods.

Main Results:

  • Demonstrated the feasibility of building a structural genomics engine using diverse pocket conformations and ensemble docking.
  • The engine can predict interactions for previously uncharacterized protein binding sites and chemical scaffolds.
  • This structure-based approach contrasts with traditional ligand-activity-based methods.

Conclusions:

  • The developed engine facilitates de novo structure-based activity prediction.
  • This approach can significantly accelerate the discovery of potent and specific therapeutics.
  • Potential for developing therapeutics with reduced side effects through structure-based design.