ligand2.soft {UWHAM}

A dataset of binding energies with a soft-core interaction potential

Description

A dataset for protein-ligand binding with a soft energy function.

Usage

data(ligand2.soft)

Format

A data frame containing 1 column and 15000 rows.

Details

The dataset contains binding energies (in kcal/mol) for the ligand 2/FKBP complex with a soft-core interaction energy function, simulated using replica exchange with 15 lambda values (Tan et al. 2012).

Suppose that the dataset is converted to a 1000 x 15 matrix as follows.

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

The 15 columns of lig.data correspond to the 15 lambda states from smallest (lambda=0) to largest (lambda=1). The data were obtained by reordering by lambda the raw output of the molecular dynamics replicas at each observation time. 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.