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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...
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:
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...
Induced-fit Model01:13

Induced-fit Model

Most chemical reactions in cells require enzymes—biological catalysts that speed up the reaction without being consumed or permanently changed. They reduce the activation energy needed to convert the reactants into products. Enzymes are proteins, that usually work by binding to a substrate—a reactant molecule that they act upon.
Enzymes exhibit substrate specificity, meaning that they can only bind to certain substrates. This is mainly determined by the shape and chemical characteristics of...

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Related Experiment Video

Updated: May 16, 2026

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
05:08

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

Using RosettaLigand for small molecule docking into comparative models.

Kristian W Kaufmann1, Jens Meiler

  • 1Department of Chemistry, Vanderbilt University, Nashville, Tennessee, United States of America.

Plos One
|December 15, 2012
PubMed
Summary
This summary is machine-generated.

RosettaLigand successfully identified native-like binding modes in 21 of 30 protein complexes. Template selection based on ligand occupancy, not sequence identity, improved docking success for small molecule drug discovery.

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Modeling Ligands into Maps Derived from Electron Cryomicroscopy
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Modeling Ligands into Maps Derived from Electron Cryomicroscopy

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

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Related Experiment Videos

Last Updated: May 16, 2026

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
05:08

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

Modeling Ligands into Maps Derived from Electron Cryomicroscopy
09:30

Modeling Ligands into Maps Derived from Electron Cryomicroscopy

Published on: July 19, 2024

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

Area of Science:

  • Computational biology
  • Structural bioinformatics
  • Drug discovery

Background:

  • Small molecule docking into protein models is crucial for understanding protein function and developing therapeutics.
  • Comparative protein models are increasingly used when experimental structures are unavailable.

Purpose of the Study:

  • To benchmark RosettaLigand's performance for docking small molecules into comparative protein models.
  • To identify factors influencing successful docking predictions.

Main Methods:

  • Docking simulations using RosettaLigand were performed on 30 protein-ligand complexes.
  • Comparative models from CASP8 and additional complexes were utilized.
  • Template selection strategies were evaluated.

Main Results:

  • RosettaLigand found native-like binding modes in the top ten predictions for 21 out of 30 cases.
  • Successful docking was correlated with template selection based on ligand occupancy.
  • Sequence identity between template and target did not significantly improve results.
  • Native-like binding modes typically exhibited normalized binding energy < -0.4.

Conclusions:

  • RosettaLigand is effective for small molecule docking into comparative protein models.
  • Ligand occupancy in templates is a key factor for successful docking.
  • The findings guide the application of computational docking in drug development.