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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...
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...
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,...
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...

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Updated: May 26, 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

Rosetta Ligand docking with flexible XML protocols.

Gordon Lemmon1, Jens Meiler

  • 1Department of Chemistry, Vanderbilt University, Nashville, TN, USA.

Methods in Molecular Biology (Clifton, N.J.)
|December 21, 2011
PubMed
Summary
This summary is machine-generated.

RosettaLigand software accurately predicts protein-small molecule interactions. Its latest version enhances ligand docking with new features for improved flexibility and user control.

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Last Updated: May 26, 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

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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

Published on: June 20, 2025

Area of Science:

  • Computational biology
  • Structural bioinformatics
  • Drug discovery

Background:

  • Predicting protein-ligand interactions is crucial for drug discovery.
  • Accurate prediction of binding interfaces aids in understanding molecular mechanisms.
  • RosettaLigand has been a key tool in this field.

Purpose of the Study:

  • To introduce the latest advancements in RosettaLigand software.
  • To highlight new features enhancing ligand docking capabilities.
  • To showcase the software's performance in predicting binding interfaces.

Main Methods:

  • Utilizing RosettaLigand for predicting protein-small molecule interactions.
  • Benchmarking prediction accuracy against crystal structures (70% within 2Å RMSD).
  • Implementing new features: simultaneous multi-ligand docking, fragment-based ligand representation, interface redesign, and XML scripting.

Main Results:

  • Demonstrated high accuracy in predicting binding interfaces (70% within 2Å RMSD).
  • Introduced simultaneous multi-ligand docking for complex systems.
  • Enabled flexible ligand representation using fragments.
  • Incorporated dynamic interface redesign during the docking process.
  • Provided full user control via an XML-based interface.

Conclusions:

  • The latest RosettaLigand release offers significant improvements for predicting protein-ligand interactions.
  • New features enhance flexibility, control, and efficiency in molecular docking.
  • The software remains a powerful tool for computational drug design and structural biology research.