Molecular Modeling and Simulations

MOE’s internal representation of organic chemical structures and flexible architecture provide a solid foundation for molecular modeling and computational chemistry. Intuitive molecular editors, file format handling, choice of validated forcefields, powerful modeling applications and customizability make MOE the most flexible molecular modeling environment in the industry.

Molecular Builders and Data Import/Export Create or edit small molecules, proteins, carbohydrates, DNA and crystal structures using a variety of molecular builders. Import and export molecular structure information, and other data, in many standard file formats. Use SD pipeline command line tools for compound filtering, descriptor calculation and structure depiction directly on SD files. An interface to Corina from Molecular Networks GmbH is provided for creating 3D conformations.

Molecular Mechanics and Dynamics MOE contains an integrated multiprocessor forcefield engine with open parameterization. Parameters for AMBER ’89/’94/’99, CHARMM22/27, MMFF94(s), OPLS-AA and Engh-Huber models are included with the distribution. Three large-scale energy minimization algorithms are available, and distance, angle and torsion angle constraints can be imposed. Atomistic NVE, NVT, NPT and NPH molecular dynamics simulations can be conducted, optionally including atomic wall restraints and tethers.

Implicit Solvent Electrostatics Simulate and understand solvation effects without explicit treatment of water molecules using implicit solvent electrostatics. All forcefield parameter sets include a Generalized Born implicit solvent model or reaction field electrostatics model. The full non-linear Poisson-Boltzmann equation can be solved using a fast multi-grid algorithm providing for modeling of mobile implicit ions effects.

Conformational Analysis Perform a conformational analysis using a Molecular Dynamics, Stochastic or Systematic search methodology (with full choice of forcefield). Use a fragment-based High Throughput methodology for construction of large conformation databases. Visualize and analyze the resulting ensembles of conformations in the MOE database viewer.

Flexible Alignment of Small Molecules Perform a 3D alignment (or superposition) of known and putative ligands to deduce structural requirements for biological activity. This is especially useful if detailed structural information of a receptor is not available. MOE uses an all-atom flexible alignment procedure that combines a forcefield and a 3D similarity function based upon Gaussian descriptions of shape and pharmacophore features to produce an ensemble of possible alignments of a collection of small molecules.

Diffraction Simulation Predict the results of X-Ray, Neutron or Electron diffraction experiments in gas, amorphous liquid, powder or single crystal phases using diffraction simulations. Display structure factor data in a variety of intensity plots.

Quantum Calculations MOE provides interfaces to popular ab initio, semi-empirical and density functional codes such as GAMESS, Gaussian, ADF, MOPAC and MOPAC 2007. Use a graphical interface to configure a calculation and view results such as electron density contours, molecular orbital plots, energy level diagrams and other properties. Use MOE/smp to conduct the calculations on collections of compounds in parallel.