Molecular Modeling & 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.

MMFF, AMBER, CHARMM Forcefields 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.

Simulate and understand solvation effects using implicit solvent electrostatics and explicit waters. 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.

Molecular Mechanics & Dynamics 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.

Conformation Generation, Analysis, & Clustering 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.

An integrated application for active site analysis. Build Molecular Surfaces colored by properties, predict Contact Preferences using statistical knowledge-based potentials and calculate Electrostatic Maps using the non-linear Poisson-Boltzmann equation. Identify steric limits, regions for ligand modification and understand receptor recognition preferences.

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.