Paper Citing NAMD - Abstract
Lauro, G.; Ferruz, N.; Fulle, S.; Harvey, M. J.; Finn, P. W.; De Fabritiis, G.
Reranking Docking Poses Using Molecular Simulations and Approximate Free Energy Methods
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 54:2185-2189, AUG 2014
Fast and accurate identification of active compounds is essential for effective use of virtual screening workflows. Here, we have compared the ligand-ranking efficiency of the linear interaction energy (LIE) method against standard docking approaches. Using a trypsin set of 1549 compounds, we performed 12,250 molecular dynamics simulations. The LIE method proved effective but did not yield results significantly better than those obtained with docking codes. The entire database of simulations is released.
