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Ligand Binding Sites02:40

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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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Cooperative allosteric transitions can occur in multimeric proteins, where each subunit of the protein has its own ligand-binding site. When a ligand binds to any of these subunits, it triggers a conformational change that affects the binding sites in the other subunits; this can change the affinity of the other sites for their respective ligands. The ability of the protein to change the shape of its binding site is attributed to the presence of a mix of flexible and stable segments in the...
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GLIMPSED: An Improved Docking Protocol for Cognate Docking.

Andrea Rizzi1, Andrea Ciacci2, Anna Maria Capelli3

  • 1Chiesi Farmaceutici S.p.A. Largo Belloli, 11 A, Parma, Italy. a.rizzi@chiesi.com.

Molecular Informatics
|August 23, 2016
PubMed
Summary
This summary is machine-generated.

A new docking protocol, GLIMPSED, improves ligand pose prediction accuracy by considering binding site exposure. This method offers a statistically significant, albeit small, improvement over standard Glide SP for drug discovery research.

Keywords:
Astex diverse setCognate dockingGlideStatistical comparisons

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Area of Science:

  • Computational chemistry
  • Molecular modeling
  • Drug discovery

Background:

  • Glide SP is a standard molecular docking protocol.
  • Binding site characteristics can influence docking accuracy.
  • Ligand pose prediction is crucial for virtual screening.

Purpose of the Study:

  • To evaluate and improve the cognate docking performance of Glide.
  • To develop a protocol that accounts for binding site exposure.
  • To enhance the accuracy of ligand pose prediction in molecular docking.

Main Methods:

  • Utilized the Astex diverse set for docking performance evaluation.
  • Developed GLIMPSED protocol, adapting Glide SP based on SiteMap binding site exposure.
  • Employed MM-GBSA rescoring for solvent-exposed binding sites.
  • Compared GLIMPSED and Glide SP using Hawkins et al. metrics.

Main Results:

  • Standard Glide SP achieved an 85.7% success rate.
  • GLIMPSED achieved an 89.3% success rate, a statistically significant improvement.
  • SiteMap binding site exposure was identified as a key parameter for protocol selection.
  • Cohen's effect size test indicated a small but non-trivial superiority for GLIMPSED.

Conclusions:

  • The SiteMap binding site exposure parameter is a valuable guideline for choosing docking protocols.
  • GLIMPSED offers enhanced accuracy in predicting ligand binding poses, especially for solvent-exposed sites.
  • The findings support the adoption of adaptive docking strategies in drug discovery.