Molecular design software is software for molecular modeling, that provides special support for developing molecular model

Molecular model

A molecular model, in this article, is a physical model that represents molecules and their processes. The creation of mathematical models of molecular properties and behaviour is molecular modelling, and their graphical depiction is molecular graphics, but these topics are closely linked and each...

s de novo.

In contrast to the usual molecular modeling programs such as the molecular dynamics

Molecular dynamics

Molecular dynamics is a computer simulation of physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a period of time, giving a view of the motion of the atoms...

 and quantum chemistry

Quantum chemistry

Quantum chemistry is a branch of chemistry whose primary focus is the application of quantum mechanics in physical models and experiments of chemical systems...

 programs, such software directly supports the aspects related to the construction of molecular models:

• Molecular graphics
  Molecular graphics
  Molecular graphics is the discipline and philosophy of studying molecules and their properties through graphical representation. IUPAC limits the definition to representations on a "graphical display device"...
  
  
• interactive molecular drawing and conformational editing
  Molecule editor
  A molecule editor is a computer program for creating and modifying representations of chemical structures.Molecule editors can manipulate chemical structure representations in either two- or three-dimensions. Two-Dimensional editors generate output used as illustrations or for querying chemical...
  
  
• building of polymeric molecules, crystals and solvated systems
  Solvation
  Solvation, also sometimes called dissolution, is the process of attraction and association of molecules of a solvent with molecules or ions of a solute...
  
  
• partial charges development
• geometry optimization
  Optimization (mathematics)
  In mathematics, computational science, or management science, mathematical optimization refers to the selection of a best element from some set of available alternatives....
  
  
• support for the different aspects of Force Field
  Force field (chemistry)
  In the context of molecular modeling, a force field refers to the form and parameters of mathematical functions used to describe the potential energy of a system of particles . Force field functions and parameter sets are derived from both experimental work and high-level quantum mechanical...
  
   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

Molecular mechanics

Molecular mechanics uses Newtonian mechanics to model molecular systems. The potential energy of all systems in molecular mechanics is calculated using force fields...

,
QM - Quantum mechanics

Quantum mechanics

Quantum mechanics, also known as quantum physics or quantum theory, is a branch of physics providing a mathematical description of much of the dual particle-like and wave-like behavior and interactions of energy and matter. It departs from classical mechanics primarily at the atomic and subatomic...

.
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
AMBER AMBER AMBER is a family of force fields for molecular dynamics of biomolecules originally developed by the late Peter Kollman's group at the University of California, San Francisco. AMBER is also the name for the molecular dynamics software package that simulates these force fields...				+	+			+		+	+		+		ambermd.org	Classical molecular modeling program
ArgusLab	+	+			+			+	+	+	+	+			Planaria Software	A molecular modeling, graphics, and drug design program
Ascalaph Designer Ascalaph Designer Ascalaph Designer is a general purpose molecular modelling package for molecular design and simulations. It provides a graphical environment for the common programs of quantum and classical molecular modelling NWChem, Firefly, CP2K and MDynaMix...	+	+	+	+	+	+	+	+		+	+	+	+		Agile Molecule	common molecular modeling suite
Avogadro (software) Avogadro (software) Avogadro is a molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas...	+	+			+	+		+		+	+		+		OpenMolecules.net	Extensible, free, open source molecular editor
BALLView Ball A ball is a round, usually spherical but sometimes ovoid, object with various uses. It is used in ball games, where the play of the game follows the state of the ball as it is hit, kicked or thrown by players. Balls can also be used for simpler activities, such as catch, marbles and juggling...	+	+			+	+			+	+	+		+	+	ball-project.org	Open source, extensible molecular modelling editor with real time raytracing and integrated Python interface
BOSS BOSS (molecular mechanics) BOSS is a general-purpose molecular modeling program that performs molecular mechanics calculations, Metropolis Monte Carlo statistical mechanics simulations, and semiempirical AM1, PM3, and PDDG/PM3 quantum mechanics calculations...								+		+	+	+	+		Yale University	OPLS OPLS The OPLS force field was developed by Prof. William L. Jorgensen at Purdue University and later at Yale University.-Functional form:The functional form of the OPLS force field is very similar to that of AMBER:...  inventor
DOCK DOCK The program UCSF DOCK was created in the 1980s by Irwin "Tack" Kuntz's Group, and was the first docking program. DOCK uses geometric algorithms to predict the binding modes of small molecules. Brian K. Shoichet, David A...								+	+	+	+				University of California	DOCK algorithm
eHiTS	+							+	+	+	+		+	+	SimBioSys, Inc.	eHiTS docking and virtual screening suite
Firefly (PC GAMESS) PC GAMESS PC GAMESS/Firefly is an ab initio computational chemistry program for Intel-compatible x86, x86-64 processors based on GAMESS sources. However, it has mostly been rewritten , especially in platform-specific parts , mathematic functions , and quantum chemical methods PC GAMESS/Firefly is an ab...								+		+		+	+		Moscow State University	ab initio and DFT computational chemistry program
FoldX FoldX FoldX is a protein design algorithm that uses an empirical force field. It can determine the energetic effect of point mutations as well as the interaction energy of protein complexes...								+		+	+		+		CRG	A force field for energy calculations and protein design
Lead Finder Lead Finder Lead Finder software is a computational chemistry application for modeling protein-ligand interactions. Lead Finder can be used in molecular docking studies and for the quantitative evaluation of ligand binding and biological activity...								+	+		+				MolTech	Lead Finder molecular docking package
Maestro	+	+	+	+	+	+	+	+	+	+	+	+	+		Schrodinger	A molecular modeling, visualization, and drug design program
Materials Studio Materials Studio Materials Studio is software for simulating and modeling materials developed and distributed by Accelrys, a company specializing in research software for computational chemistry, bioinformatics, cheminformatics, molecular simulation, and quantum mechanics....	+	+	+			+	+	+	+	+	+	+	+		Accelrys	software environment
MedeA	+		+			+				+	+	+			Materials Design	software environment for inorganic materials science
MOE	+	+	+	+	+	+	+	+	+	+	+	+	+		Chemical Computing Group	Molecular Operating Environment
VLifeMDS	+	+						+	+	+	+	+	+	+	VLife Sciences Technologies Pvt. Ltd.	VLife Molecular Design Suite
NAB				+						+	+				Rutgers University	molecular manipulation language for nucleic acids
PCMODEL	+		+	+	+				+	+	+	+			Serena Software Serena Software Serena Software Inc is US-based software company.Serena develops and markets products focused on managing change across information technology environments...	common molecular modeling tool
SPARTAN Spartan (software) SPARTAN is a molecular modeling and computational chemistry application from . It contains code for molecular mechanics, semi-empirical methods, ab initio models, density functional models, post-Hartree-Fock models, and thermochemical recipes including T1....	+	+		+	+		+	+		+	+	+			Wavefunction	molecular modeling tool with molecular mechanics and quantum chemical engines
StruMM3D (STR3DI32)	+	+	+	+	+	+	+	+	+	+	+				Exorga Software	molecular modeling tool
TINKER TINKER TINKER is a computer software application for molecular dynamics simulation with a complete and general package for molecular mechanics and molecular dynamics, with some special features for biopolymers...					+			+		+	+				Washington University	freeware, tools for protein design

See also

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.