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2
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ShareScore release 0.9.0
Dataset results
2 results for “conformation space networks”
BPTF-AU1 conformation space network
<p><strong>This dataset contains:</strong></p> <ul> <li><em>allstates.gexf</em>: a graph file describing the nodes and edges of the configuration space network. Nodes are clusters of molecular conformations, and edges are the connections between them, derived from molecular dynamics trajectories. This file also contains properties for each node: minimum ligand-protein distance (<em><strong>mind</strong></em>), ligand solvent accessible surface area (<em><strong>sasa</strong></em>), number of observations from A-initialized simulations (<em><strong>na</strong></em>), number of observations from B-initialized simulations (<em><strong>nb</strong></em>), total number of observations (<em><strong>ntot</strong></em>), free energy prediction (<em><strong>eig_wt_final_sym</strong></em>). This file can be opened in network analysis programs (e.g. Gephi).</li> <li><em>bptf_au1.pdb</em>: a PDB file containing the BPTF protein and the AU1 molecule</li> <li><em>clust90.dcd</em>: a trajectory composed of randomly selected structures from cluster 90, which was predicted to be the most stable cluster according to the free energy</li> <li><em>allclusts.tgz</em>: an archive file containing a (randomly selected) PDB structure for every cluster in the network</li> </ul>
Representative structures for Trypsin-Benzamidine conformation-space network
<p>These structures were used for the analysis presented in the paper "Multiple Ligand Unbinding Pathways and Ligand-Induced Destabilization Revealed by WExplore" published in Biophysical Journal, 112, February 28, 2017. There is a tar ball (allframes.tgz) containing 4000 structures in PDB format, as well as a PDF file of the network with labels for each of the 4000 states (network_labels.pdf). Unpack the tar ball with: "tar xzf allframes.tgz".</p> <p> </p>
ScienceDex guides
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