Molecular dynamics simulations and a multi-tiered clustering scheme improve function prediction. In this project, we plan to provide the 1 nanosecond trajectories that were generated for predicting calcium-binding sites for 5 different proteins.
Most function prediction algorithms use data from experimental techniques, such as x-ray crystallography, which show a molecule’s structure at one particular moment in time.
However, the molecule may not be in a functional configuration at that instant, resulting in incorrect predictions. We show that using molecular dynamics simulations along with a multi-tiered clustering scheme that we developed, you can increase the accuracy of your predictions of molecular functional sites.
We plan to provide the 1 nanosecond trajectories that were generated for this work. Trajectories for 22 different starting configurations will be available: a calcium-bound (HOLO) and non-calcium-bound (APO) version of 11 different proteins.