Moleculare Modeling and Simulations

Molecular Builders Build small molecules, carbohydrates, proteins, DNA and crystal structures in 3D with a collection of graphical interfaces. Chiral inversions and editing of bond lengths, angles and torsions are supported. Explicit water molecules can be added automatically and/or restricted to an active site.

Molecular Mechanics and Dynamics Perform large-scale energy minimizations using AMBER ’89/’94, MMFF94, PEFSAC95 or Engh-Huber force field parameters with an implicit solvent model. Conformational analyses include both stochastic and systematic searches (including rings). Calculate dynamics trajectories in the NVE, NVT, NPT and NPH ensembles.

Implicit Solvent Electrostatics Solve the non-linear Poisson-Boltzmann equation with a non-linear multi-grid method to produce the implicit solvent electrostatics field. The resulting field can be visualized with iso-surfaces or color coded molecular surfaces.

Molecule Alignment Align a collection (flexibly or rigid-body) of small molecules that are presumed to have similar biological activity. Alignments are useful for the elucidation of pharmacophores, input to comparative field analysis and template forcing.

Polymer Property Prediction Predict over 50 properties of polymers using QSPR methods and models. Properties include amorphous volume, heat capacity, cohesive energies, solubilities, glass transition temperature, refractivity, and mechanical properties.

Diffraction Simulation Simulate X-Ray, Neutron and Electron diffraction experiments. Gas, Amorphous Liquid, Powder and Single Crystal diffractions are supported. Structure factor data can be displayed in a variety of intensity plots.