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  • Estimation of relative residence times of protein-ligand complexes using τ-Random Acceleration Molecular Dynamics (τRAMD), implementation in NAMD
  • Data exploration and linear regression of a kinetic dataset using R
  • Compartmental modelling and simulation in Berkeley Madonna
  • Prediction of the rate of formation of a protein-protein complex
  • Generation of Quantitative structure-kinetics relationships (QSKRs) using Comparative Binding Energy (COMBINE) Analysis
  • Estimation of relative residence times of protein-ligand complexes using τ-Random Acceleration Molecular Dynamics (τRAMD), implementation in Gromacs
  • Estimation of relative residence times of protein-ligand complexes using Scaled Molecular Dynamics (ScMD, BikiNetics)

Tutorials

To the left you can find indepth tutorials that aim to introduce newcomers to the methods required to reproduce some of the example cases.

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