Analysis of Free Energy Calculations

Analysis of Free Energy Calculations

Analysis of Free Energy Calculations

Analysis of binding free energy is an important content in computer-aided drug design. CD BioSciences is committed to developing direct and computationally efficient methods to provide clients with analysis of free energy calculations and accelerate their progress in virtual high throughput screening (vHTS), which is a powerful approach to identify hits in drug discovery.


Drug discovery is a multi-objective, multi-parameter optimization process, with binding affinity and biological potency being the primary indicators of a wide range of drug-forming properties. In recent years, with the spread of virtual drug discovery models, the prediction and optimization of drug-forming properties of compounds have become more intelligent and efficient. Currently, physics-based free energy simulations have become a powerful tool for drug molecule discovery, structure optimization and preparation process optimization.

As the core technology of drug structure optimization, free energy simulation can strictly calculate the properties of conformational equilibrium, solvation and binding free energy. The purpose of free energy calculation is to explain the physical basis of molecular recognition and binding and predict the binding ability of molecules in the system. The development of effective strategies for accurately predicting binding free energy will help to promote the progress from drug discovery to physical property prediction and structure-function research.

Fig.1 Schematic diagram of different approaches for free energy calculations. (Barros, 2022)Fig.1 Schematic diagram of different approaches for free energy calculations. (Barros, 2022)

Our Services

Our researchers have developed efficient computational methods for calculating the binding energies of the different molecules required for virtual screening. We help our customers analyze free energy calculations by providing a range of rigorous simulation methods. Our services include but are not limited to:

  • We offer multi-scale free energy simulations to calculate free energies.
  • Obtaining free energies at the quantum mechanical (QM) scale.
  • Obtaining free energies at the AT (or molecular mechanics, MM) scale.
  • Obtaining free energies at the coarse-grained (CG) scale.
  • We offer free energy perturbation calculations (FEP) to assess the binding strength of drug small molecules to targets and to calculate the relative receptor-ligand binding free energy.
  • Estimation of the state of the ligand before and after binding to the receptor by absolute binding free energy (ABFE) calculations.
  • Estimation of the binding state of the target site to different ligands by relative binding free energy (RBFE) calculations.
  • Analysis of free energy calculations.
  • Subsampling of the data and retention of irrelevant samples.
  • Calculation of free energy differences along with the corresponding statistical errors.
  • Textual and graphical output of the calculated data.
  • Check for convergence and determine the equilibrium part of the simulation.


  • Estimation of the binding capacity of a compound to a target site
  • Prediction of the structure of bound transition intermediates
  • Combined kinetic analysis

With a dedicated research team consisting of experts in a variety of fields including biophysics and computational biology, CD BioSciences is well placed to provide clients with services for the calculation and analysis of free energy in drug discovery. We have built up a wealth of experience in the biotechnology and pharmaceutical industry, which helps us to provide you with professional scientific services. If you are interested in our services, please contact us for more details.


  1. Barros, E. P.; et al. Recent developments in multiscale free energy simulations. Current opinion in structural biology. 2022, 72: 55-62.
For research use only, not intended for any clinical use.
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