ligand2.hard {UWHAM} | R Documentation |
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.