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

Notes and references

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.
Journal of Chemical Information and Modeling
Journal of Computational Chemistry

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Molecular design software

Contents

Comparison of software covering the major aspects of molecular design

Notes and references

See also

External links