Molecular design software
# Molecular design software

Molecular design software is notable software for molecular modeling, that provides special support for developing molecular models de novo.

In contrast to the usual molecular modeling programs, such as for molecular dynamics and quantum chemistry, such software directly supports the aspects related to constructing molecular models, including:

* Molecular graphics
* interactive molecular drawing and conformational editing
* building polymeric molecules, crystals, and solvated systems
* partial charges development
* geometry optimization
* support for the different aspects of force field development

## Comparison of software covering the major aspects of molecular design

* 3D – molecular graphics
* Mouse – drawing molecule by mouse
* Poly – polymer building
* DNA – nucleic acid building
* Pept – peptide building
* Cryst – crystal building
* Solv – solvent addition
* Q – partial charges
* Dock – docking
* Min – optimization
* MM – molecular mechanics
* QM – quantum mechanics
* FF – supports force field development
* QSAR – 2D, 3D, and group QSAR
* FBLD - Fragment Based Ligand Design
* FE - Free Energy approximations
* SN - Space Navigation

| | 3D | Mouse | Poly | DNA | Pept | Cryst | Solv | Q | Dock | Min | MM | QM | FF | QSAR | FBLD | FE | Comments |
| - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
| Abalone | Yes | Yes | Yes | Yes | Yes | Yes | Yes | Yes | No | Yes | Yes | Yes | Yes | No | | | Biomolecular graphics environment: macromolecule builders, GPU accelerated MD |
| AMBER | No | No | No | Yes | Yes | No | No | Yes | No | Yes | Yes | No | Yes | No | | Yes | Classical molecular modeling program |
| Ascalaph Designer | Yes | Yes | Yes | Yes | Yes | Yes | Yes | Yes | No | Yes | Yes | Yes | Yes | No | | | Common molecular modeling suite |
| BOSS | No | No | No | No | No | No | No | Yes | No | Yes | Yes | Yes | Yes | No | | | OPLS inventor |
| Discovery Studio | Yes | Yes | Yes | Yes | Yes | Yes | Yes | Yes | Yes | Yes | Yes | Yes | Yes | Yes | | | Molecule modeling environment for both small and macro molecular systems |
| DOCK | No | No | No | No | No | No | No | Yes | Yes | Yes | Yes | No | No | No | | | DOCK algorithm |
| Firefly (PC GAMESS) | No | No | No | No | No | No | No | Yes | No | Yes | No | Yes | Yes | No | | | Ab initio and DFT computational chemistry program |
| FoldX | No | No | No | No | No | No | No | Yes | No | Yes | Yes | No | Yes | No | | | A force field for energy calculations and protein design |
| Lead Finder | No | No | No | No | No | No | No | Yes | Yes | No | Yes | No | No | No | | | Molecular docking package |
| Materials Studio | Yes | Yes | Yes | No | No | Yes | Yes | Yes | Yes | Yes | Yes | Yes | Yes | No | | | Software environment |
| Molecular Operating Environment (MOE) | Yes | Yes | Yes | Yes | Yes | Yes | Yes | Yes | Yes | Yes | Yes | Yes | Yes | Yes | Yes | | Platform for molecular modelling / drug discovery applications, programmed in Scientific Vector Language to enable application customisation and development |
| Rosetta (RosettaCommons) | No | No | Yes | Yes | Yes | Yes | Yes | Yes | Yes | Yes | Yes | No | Yes | No | | | A suite for macromolecule modeling. Algorithms for modeling and analysis of protein structures. Key advances in de novo protein design, enzyme design, ligand docking, structure prediction |
| SAMSON | Yes | Yes | No | No | No | Yes | No | No | Yes | Yes | Yes | Yes | Yes | No | | | Computational nanoscience (life sciences, materials, etc.); modular architecture, modules are termed Elements; free |
| Scigress | Yes | Yes | Yes | No | Yes | Yes | Yes | Yes | Yes | Yes | Yes | Yes | Yes | Yes | | | General purpose molecular modeling suite |
| Spartan | Yes | Yes | No | Yes | Yes | No | Yes | Yes | No | Yes | Yes | Yes | No | No | | | Molecular modeling tool with molecular mechanics and quantum chemical engines |
| Tinker | No | No | No | No | Yes | No | No | Yes | No | Yes | Yes | No | No | No | | | Tools for protein design; freeware |
| Winmostar | Yes | Yes | Yes | No | No | Yes | Yes | Yes | No | Yes | Yes | Yes | Yes | No | | | Molecular modeling and visualizing program for materials science |
| Schrödinger | Yes | Yes | Yes | Yes | Yes | Yes | Yes | Yes | Yes | Yes | Yes | Yes | Yes | Yes | Yes | Yes | Molecular modeling platform for both life and materials science |
