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 the molecular dynamics and quantum chemistry programs, such software directly supports the aspects related to the construction of molecular models:

• Molecular graphics
• interactive molecular drawing and conformational editing
• building of polymeric molecules, crystals and solvated systems
• partial charges development
• geometry optimization
• support for the different aspects of Force Field development
• etc.

Comparative table of packages 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 - Support for Force Field development. QSAR - 2D, 3D and Group QSAR.

	3D	Mouse	Poly	DNA	Pept	Cryst	Solv	Q	Dock	Min	MM	QM	FF	QSAR	Homepage	Comments
Abalone	+	+	+	+	+	+	+	+		+	+	+	+		biomolecular-modeling.com	Bio-molecular graphics environment: macromolecular builders, GPU accelerated MD.
AMBER				+	+			+		+	+		+		ambermd.org	Classical molecular modeling program
Ascalaph Designer	+	+	+	+	+	+	+	+		+	+	+	+		Agile Molecule	common molecular modeling suite
BOSS								+		+	+	+	+		Yale University	OPLS inventor
DENEB	+	+	+	+	+	+	+			+		+			Atelgraphics	A atomic scale modeling software for full cycle design, calculation and analysis. Interfaces with DFT engines.
Discovery Studio	+	+	+	+	+	+	+	+	+	+	+	+	+	+	Dassault Systèmes BIOVIA	A molecular modeling environment for both small and macromolecular systems
DOCK								+	+	+	+				University of California	DOCK algorithm
Firefly (PC GAMESS)								+		+		+	+		Moscow State University	ab initio and DFT computational chemistry program
FoldX								+		+	+		+		CRG	A force field for energy calculations and protein design
Lead Finder								+	+		+				MolTech	Lead Finder molecular docking package
Maestro (Schrödinger)	+	+	+	+	+	+	+	+	+	+	+	+	+	+	Schrodinger	Molecular modeling and visualization program for drug design and materials science
Materials Studio	+	+	+			+	+	+	+	+	+	+	+		Dassault Systèmes BIOVIA	software environment
SAMSON	+	+							+	+	+	+	+		SAMSON Connect	Free. Computational nanoscience (life sciences, materials, etc.). Modular architecture (SAMSON Elements are modules for SAMSON).
SCIGRESS	+	+	+		+	+	+	+	+	+	+	+	+	+	Fujitsu	General purpose molecular modeling suite
SPARTAN	+	+		+	+		+	+		+	+	+			Wavefunction	molecular modeling tool with molecular mechanics and quantum chemical engines
TINKER					+			+		+	+				Washington University	freeware, tools for protein design

Notes and references

See also

• Molecule editor
• Molecular modelling
• Molecular modelling on GPU
• Protein design
• Drug design
• Force field
• Force field implementation
• Nucleic acid simulation software
• List of molecular graphics systems
• Software for molecular mechanics modeling
• 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.