Automatic selection of near-native protein-ligand conformations using a hierarchical clustering and volunteer computing
Trilce Estrada, Roger S. Armen, Michela Taufer · 2010
Docking simulations are commonly used to understand drug binding and require the search of a large space of proteinligand conformations. Cloud and volunteer computing enable computationally expensive docking simulations at a rate never seen before but at the same time require scientists to deal with larger datasets. When analysing these datasets, a common practice is to reduce the resulting number of candidates up to 10 to 100 conformations based on energy values and then leave the scientists with the tedious task of subjectively selecting a possible near-native ligand. Scientists normally perform this task manually by using visual tools. Not only the manual process still depends on inaccurate energy scoring but also can be highly error-prone.