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The Equilibrium Binding Constant and Binding Strength02:18

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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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Computation of Atmospheric Concentrations of Molecular Clusters from ab initio Thermochemistry
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Large-scale binding affinity calculations on commodity compute clouds.

S J Zasada1, D W Wright1, P V Coveney1

  • 1Centre for Computational Science, University College London, 20 Gordon Street, London WC1H 0AJ, UK.

Interface Focus
|November 12, 2020
PubMed
Summary
This summary is machine-generated.

We developed a binding affinity calculator workflow using molecular dynamics simulations to rapidly predict drug-protein binding. This computational tool automates calculations on cloud platforms for drug discovery and personalized medicine.

Keywords:
clouddrug bindingfree energymolecular dynamicsworkflow

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Area of Science:

  • Computational chemistry
  • Biophysics
  • Drug discovery

Background:

  • Calculating binding affinities is crucial for drug discovery and personalized medicine.
  • Free energy calculations using molecular dynamics (MD) simulations offer a promising approach.

Purpose of the Study:

  • To develop and present a software infrastructure for automating binding affinity calculations.
  • To enable reliable prediction of binding affinities on relevant timescales using cloud computing.

Main Methods:

  • Utilized molecular dynamics (MD) simulations and ensemble averages.
  • Developed a "binding affinity calculator" workflow for automation.
  • Leveraged commodity cloud computing platforms with multi-core and GPU acceleration.

Main Results:

  • Successfully automated the binding affinity calculation workflow.
  • Demonstrated the application of the workflow to two free energy methods.
  • Enabled predictions on timescales relevant for drug discovery applications.

Conclusions:

  • The developed binding affinity calculator workflow automates complex free energy calculations.
  • This approach enhances the speed and accuracy of predicting compound-protein interactions.
  • Facilitates applications in drug discovery and personalized medicine through accessible cloud computing.