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  • ligand
  • Here, we have been able to quantitatively reconstruct the complete binding process of the enzyme-inhibitor complex trypsin-benzamidine by performing 495 molecular dynamics simulations of free ligand binding of 100 ns each, 187 of which produced binding events with an rmsd less than 2 Å compared to the crystal structure. (pnas.org)
  • The simulations also allowed us to elucidate the local side-chain dynamical variations in ligand-bound mutant receptors. (springer.com)
  • Biomolecular
  • MDMap is an automated system to visualize MD simulations as state-transition diagrams, and can replace the current tedious manual layouts of biomolecular folding landscapes with an automated tool. (umd.edu)
  • coarse
  • Using Molecular Dynamic (MD) simulation and a coarse grain model, a series of bilayers with various bilayer structure (single bilayer, parallel bilayer and cylindrical bilayer) and similar composition to biological axonal membrane were simulated. (diva-portal.org)
  • conformational
  • MDMap automatically determines potential intermediate conformations and the transitions amongst them by analyzing the conformational space explored by the MD simulation. (umd.edu)
  • visualization
  • We believe this system could provide a road-map for the visualization of other stochastic time-varying simulations in a variety of different domains. (umd.edu)