Molecular design software

Molecular design software is 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

	3D	Mouse	Poly	DNA	Pept	Cryst	Solv	Q	Dock	Min	MM	QM	FF	QSAR	Website	Comments
Abalone	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	No	Yes	Yes	Yes	Yes	No	biomolecular-modeling.com	Biomolecular graphics environment: macromolecule builders, GPU accelerated MD
AMBER	No	No	No	Yes	Yes	No	No	Yes	No	Yes	Yes	No	Yes	No	ambermd.org	Classical molecular modeling program
Ascalaph Designer	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	No	Yes	Yes	Yes	Yes	No	Agile Molecule	Common molecular modeling suite
BOSS	No	No	No	No	No	No	No	Yes	No	Yes	Yes	Yes	Yes	No	Yale University	OPLS inventor
DENEB	Yes	Yes	Yes	Yes	Yes	Yes	Yes	No	No	Yes	No	Yes	No	No	Atelgraphics	Atom-scale modeling software for full cycle design, calculation, and analysis; interfaces with DFT engines
Discovery Studio	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Dassault Systèmes BIOVIA	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	University of California	DOCK algorithm
Firefly (PC GAMESS)	No	No	No	No	No	No	No	Yes	No	Yes	No	Yes	Yes	No	Moscow State University	Ab initio and DFT computational chemistry program
FoldX	No	No	No	No	No	No	No	Yes	No	Yes	Yes	No	Yes	No	CRG	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	MolTech	Molecular docking package
Maestro (Schrödinger)	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Schrodinger	Molecular modeling and visualizing program for drug design and materials science
MAPS	Yes	Yes	Yes	No	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Scienomics	Multi-scale, multi-paradigm, extensible platform that allows to build, simulate and analyze complex materials.
Materials Studio	Yes	Yes	Yes	No	No	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	No	Dassault Systèmes BIOVIA	Software environment
SAMSON	Yes	Yes	No	No	No	No	No	No	Yes	Yes	Yes	Yes	Yes	No	SAMSON Connect	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	Fujitsu	General purpose molecular modeling suite
Spartan	Yes	Yes	No	Yes	Yes	No	Yes	Yes	No	Yes	Yes	Yes	No	No	Wavefunction	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	Washington University	Tools for protein design; freeware

Notes and references

See also

• 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

External links

• 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.