A dataset of binding energies obtained with a conventional interaction potential

Description

A dataset for protein-ligand binding with an unmodified energy function.

Usage

data(ligand2.hard)

Format

A data frame containing 1 column and 18000 rows.

Details

The dataset contains binding energies (in kcal/mol) for the ligand 2/FKBP complex with an unmodified energy function, simulated using replica exchange with 18 lambda values (Tan et al. 2012).

Suppose that the dataset is converted to a 1000 x 18 matrix as follows.

  data(ligand2.hard)
  lig.data <- matrix(ligand2.hard$V1, nrow=1000)

The 18 columns of lig.data correspond to the raw output of the 18 replicas. A replica is defined as a continuous replica exchange molecular dynamics thread with variable lambda (exchanges are performed by swapping lambda values rather than coordinates). The 1000 rows represent as many sequential time points during the replica exchange trajectory. Each row contains binding energies from each replica taken at the same simulation time (synchronous sampling).

References

Tan, Z., Gallicchio, E., Lapelosa, M., and Levy, R.M. (2012) "Theory of binless multi-state free energy estimation with applications to protein-ligand binding," Journal of Chemical Physics, 136, 144102.

Results