Simulated trajectory ensembles for the closed-to-open transition of adenylate kinase from DIMS MD and FRODA

The macromolecular conformational transition between the closed conformation of apo-adenylate kinase from E. coli (EcAdK) to the open conformation was sampled with two methods: (1) dynamic importance sampling molecular dynamics (DIMS MD), and (2) Framework Rigidity Optimized Dynamics Algorithm (FRODA). Each ensemble of independently generated paths contains 200 trajectories in the CHARMM DCD format.<br><br>Data are from: Seyler SL, Kumar A, Thorpe MF, Beckstein O (2015) <i>Path Similarity Analysis: A Method for Quantifying Macromolecular Pathways</i>. PLoS Comput Biol 11(10): e1004568. https://doi.org/10.1371/journal.pcbi.1004568 (see there for more details).<br>Each tar file contains a directory <i>trajectories</i> containing the DCD files and a directory <i>topologies</i> with files that include information about the atoms (CHARMM PSF format or PDB format).<br><br><b>DIMS.tar.gz</b>: DIMS AdK (implicit solvent) with dynamic importance sampling MD from closed (1AKE) to open (4AKE). CHARMM 22 force field.<code> Topology file: adk4ake.psf <br></code><code><br></code> <b>FRODA.tar.gz</b>: FRODA AdK with geometric targeting on a rigid decomposition (FRODA server); closed (1AKE) to open (4AKE)<code>. Topology file: 1ake.pdb<br></code><code><br></code>