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Molecular design software

From Wikipedia, the free encyclopedia

Molecular design software is notable software formolecular modeling, that provides special support for developingmolecular modelsde novo.

In contrast to the usual molecular modeling programs, such as formolecular dynamics andquantum chemistry, such softwaredirectly supports the aspects related to constructing molecular models, including:

Molecular graphics
interactive molecular drawing andconformational editing
building polymeric molecules, crystals, andsolvated systems
partial charges development
geometry optimization
support for the different aspects offorce 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	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	Yes	No	No	Yes	Yes	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