Significant Capabilities

Evaluate molecules for binding sites, reactive sites, and pockets, using our exact charge distribution profiles and optimized molecular structures.

Calculate optimized molecular structures for molecules not in existing databases. Reduce your reliance on molecular structure databases.

Edit protein structures by auto-detecting missing hydrogens, and use our bond order correction tool for complex molecules like PDB heterogens.

Calculate dipole moments and rotation barrier heights for molecular conformation changes.

Convert between SMILES, MOL, and PDB file formats.

Generate optimized 3D structures for molecules with complicated fused rings from SMILES input.

Technical Features

• Energy minimization including the following algorithms: Steepest Descent, Steepest Descent with dihedral angles, Simulated Annealing, Genetic Algorithm.

• Automatically adds hydrogen atoms to molecules to satisfy valence.

• Automatic generation of 3D coordinates for molecules including complex cyclic molecules.

• Turn on/off the chains in modeled and displayed proteins.

Modeling Features

• Exact structure and energy of molecules, atoms and bonds
  contained in the molecules.

• Bio-pharma relevant molecular library.

• Amino acid template to facilitate modeling proteins.

• Base pair templates to facilitate modeling DNA and RNA.

• Calculate molecular dipole moment.

• Molecular conformation energy calculation.

• Display charge profile of the molecule surface.

• Renders combinations of solved covalent bonding function groups
  (essentially all molecules except metals and ionic compounds).

• These are calculated instantly on modern desktop computers.

File Types Read/Write and Import/Export

• PDB file format.

• MOL file format.

• SMILES.

• convert MOL to PDB.

• MOL SD.

• CP and other Millsian file types.

• Multi-molecule display up to infinite sized molecule (limited by computer processor and video card capabilities).

• OpenGL graphics right-sized to the hardware.

• Rotation of the molecule to gain better view of the molecule from different angles.