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

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* 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  | SN  | Comments

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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

## Notes and references

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## See also

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* Molecule editor
* Molecular modelling
* Molecular modeling on GPUs
* Protein design
* Drug design
* Force field (chemistry)
* Comparison of force field implementations
* Comparison of nucleic acid simulation software
* Comparison of software for molecular mechanics modeling
* List of molecular graphics systems
* List of software for Monte Carlo molecular modeling
* List of software for nanostructures modeling
* Quantum chemistry computer programs
* Quantitative structure-activity relationship
* XMD, a classical molecular dynamics software

## External links

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* molecular design IUPAC term definition.
* Journal of Computer-Aided Molecular Design
* Molecular Modeling resources
* Materials modelling and computer simulation codes
* Click2Drug.org Directory of in silico (computer-aided) drug design tools.
* Journal of Chemical Information and Modeling
* Journal of Computational Chemistry