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Related Concept Videos

Ligand Binding Sites02:40

Ligand Binding Sites

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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.
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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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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:
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The two-state receptor model explains a drug's interaction with receptors, such as G protein-coupled receptors and ligand-gated ion channels, to induce or inhibit a biological response. When no natural ligands are present, a receptor exists in an equilibrium of inactive (Ri) and active (Ra) conformations. The inactive form does not produce a response, while the active form generates a basal effect known as constitutive activity.
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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
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Receptor-ligand molecular docking.

Isabella A Guedes1, Camila S de Magalhães2, Laurent E Dardenne3

  • 1Laboratório Nacional de Computação Científica (LNCC/MCT), Quitandinha, Petrópolis, RJ, 25651-075, Brazil.

Biophysical Reviews
|May 17, 2017
PubMed
Summary
This summary is machine-generated.

Molecular docking uses search algorithms and scoring functions to predict how molecules bind to targets. This review covers common methods and challenges in protein-ligand docking for drug discovery.

Keywords:
Protein-ligand dockingScoring functionsSearch algorithmsStructure-based drug design

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Area of Science:

  • Computational chemistry
  • Structural biology
  • Drug discovery

Background:

  • Molecular docking is a key computational tool in drug design.
  • It predicts binding modes and affinities of small molecules to receptor targets.
  • It is used for lead compound optimization and virtual screening.

Purpose of the Study:

  • To review common search algorithms and energy scoring functions in protein-ligand docking.
  • To summarize recent advances in molecular docking methodology.
  • To highlight challenges in predicting binding affinity.

Main Methods:

  • Review of current literature on protein-ligand docking algorithms.
  • Analysis of commonly used search algorithms (e.g., genetic algorithms, Monte Carlo).
  • Evaluation of energy scoring functions (e.g., force-field based, empirical).

Main Results:

  • Commonly used search algorithms and scoring functions are detailed.
  • Recent computational and methodological advancements are summarized.
  • Key challenges including protein flexibility and accurate binding affinity prediction are discussed.

Conclusions:

  • Molecular docking is essential for identifying novel drug candidates.
  • Further methodological developments are needed to address protein flexibility and improve binding affinity prediction.
  • Accurate prediction of binding free energy remains a significant challenge.