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University of Colorado Denver

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Computational Chemistry and Biology Core Facility

Molecular Simulations and Quantum Molecular Mechanics


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The CCB Core can perform sophisticated simulations of the potential interactions between macromolecules, ligands, cofactors, membrane surfaces, and metal ions using advanced molecular mechanics, quantum mechanics, spatial alignments, and energetic calculations.  Capabilities include:

  • Optimization and minimization of DNA, RNA, carbohydrates, lipids, proteins, peptides, and small molecules
  • Explicit or implicit solvent-based molecular mechanics and molecular dynamics simulations using a variety of atomic force fields
  • Addition of implicit membranes for refinement of transmembrane or membrane-associated protein structures
  • Prediction of protein and amino acid side chain ionization and pK values