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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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Related Experiment Video

Updated: May 1, 2026

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rDock: a fast, versatile and open source program for docking ligands to proteins and nucleic acids.

Sergio Ruiz-Carmona1, Daniel Alvarez-Garcia1, Nicolas Foloppe2

  • 1Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Barcelona, Spain; Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Spain.

Plos Computational Biology
|April 12, 2014
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Summary

rDock is a fast molecular docking software for high-throughput virtual screening (HTVS). It offers competitive speed and superior binding mode prediction, especially when using pharmacophore constraints.

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Area of Science:

  • Computational chemistry
  • Drug discovery
  • Chemical biology

Background:

  • Identifying biologically active compounds is crucial for drug discovery.
  • Molecular docking assesses small molecule-target complementarity for virtual screening (VS).

Purpose of the Study:

  • To provide an overview of the rDock molecular docking program.
  • To compare rDock's performance against AutoDock Vina and Schrödinger's Glide.

Main Methods:

  • rDock was evaluated for computational speed, binding mode prediction, and VS performance.
  • Comparisons were made against AutoDock Vina and Glide, with and without pharmacophore constraints.

Main Results:

  • rDock is computationally efficient, faster than Vina and comparable to Glide.
  • rDock and Vina show superior binding mode prediction compared to Glide.
  • rDock's VS performance is better than Vina and comparable to Glide when using pharmacophore constraints.

Conclusions:

  • rDock is a highly efficient molecular docking tool for high-throughput virtual screening.
  • The program's performance is competitive, particularly with the incorporation of pharmacophore constraints.
  • rDock is freely available under the Lesser General Public License.