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.

Data are from: Seyler SL, Kumar A, Thorpe MF, Beckstein O (2015) Path Similarity
Analysis: A Method for Quantifying Macromolecular Pathways. PLoS Comput
Biol 11(10):
e1004568.

https://doi.org/10.1371/journal.pcbi.1004568 (see there for more details).

Each tar file contains a directory trajectories containing the DCD files and a directory topologies with files that include information about the atoms (CHARMM PSF format or PDB format).

DIMS.tar.gz: DIMS
AdK (implicit solvent) with dynamic importance sampling MD
from closed (1AKE) to open (4AKE). CHARMM 22 force field. Topology file: adk4ake.psf

FRODA.tar.gz: FRODA
AdK with geometric targeting on a rigid decomposition
(FRODA server); closed (1AKE) to open (4AKE). Topology file: 1ake.pdb