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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:

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

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! 3D

! Mouse

! Poly

! DNA

! Pept

! Cryst

! Solv

! Q

! Dock

! Min

! MM

! QM

! FF

! QSAR

! FBLD

! FE

! SN

! Comments

Abalone

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| Biomolecular graphics environment: macromolecule builders, GPU accelerated MD

AMBER

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| Classical molecular modeling program

Ascalaph Designer

| {{yes}}

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| {{no}}

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| Common molecular modeling suite

BOSS

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| OPLS inventor

Discovery Studio

| {{yes}}

| {{yes}}

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| {{yes}}

| {{yes}}

| {{yes}}

| {{yes}}

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| Molecule modeling environment for both small and macro molecular systems

DOCK

| {{no}}

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| {{no}}

| {{yes}}

| {{yes}}

| {{yes}}

| {{yes}}

| {{no}}

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| DOCK algorithm

Firefly (PC GAMESS)

| {{no}}

| {{no}}

| {{no}}

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| {{no}}

| {{yes}}

| {{no}}

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| Ab initio and DFT computational chemistry program

FoldX

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| {{no}}

| {{no}}

| {{yes}}

| {{no}}

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| {{yes}}

| {{no}}

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| A force field for energy calculations and protein design

Lead Finder

| {{no}}

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| {{no}}

| {{no}}

| {{yes}}

| {{yes}}

| {{no}}

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| Molecular docking package

Materials Studio

| {{yes}}

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| {{no}}

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| {{yes}}

| {{yes}}

| {{yes}}

| {{yes}}

| {{yes}}

| {{yes}}

| {{yes}}

| {{no}}

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| Software environment

Molecular Operating Environment (MOE)

| {{yes}}

| {{yes}}

| {{yes}}

| {{yes}}

| {{yes}}

| {{yes}}

| {{yes}}

| {{yes}}

| {{yes}}

| {{yes}}

| {{yes}}

| {{yes}}

| {{yes}}

| {{yes}}

| {{yes}}

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| 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}}

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| 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}}

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| 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}}

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| General purpose molecular modeling suite

Spartan

| {{yes}}

| {{yes}}

| {{no}}

| {{yes}}

| {{yes}}

| {{no}}

| {{yes}}

| {{yes}}

| {{no}}

| {{yes}}

| {{yes}}

| {{yes}}

| {{no}}

| {{no}}

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| 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}}

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| Tools for protein design; freeware

Winmostar

| {{yes}}

| {{yes}}

| {{yes}}

| {{no}}

| {{no}}

| {{Yes}}

| {{yes}}

| {{yes}}

| {{no}}

| {{Yes}}

| {{yes}}

| {{yes}}

| {{Yes}}

| {{no}}

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| Molecular modeling and visualizing program for materials science

Schrödinger

| {{yes}}

| {{yes}}

| {{yes}}

| {{yes}}

| {{yes}}

| {{yes}}

| {{yes}}

| {{yes}}

| {{yes}}

| {{yes}}

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| {{yes}}

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| Molecular modeling platform for both life and materials science

Notes and references

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See also

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External links

  • [http://goldbook.iupac.org/MT06968.html molecular design] IUPAC term definition.
  • [https://archive.today/20130202215743/http://www.springerlink.com/content/102928/ Journal of Computer-Aided Molecular Design]
  • [http://www.biomolecular-modeling.com/Software.html Molecular Modeling resources]
  • [http://www.sklogwiki.org/SklogWiki/index.php/Materials_modelling_and_computer_simulation_codes Materials modelling and computer simulation codes]
  • [https://web.archive.org/web/20190827202106/http://click2drug.org/ Click2Drug.org] Directory of in silico (computer-aided) drug design tools.
  • [https://pubs.acs.org/journal/jcisd8 Journal of Chemical Information and Modeling]
  • [https://onlinelibrary.wiley.com/journal/1096987x Journal of Computational Chemistry]

Category:Science software

Category:Computational chemistry software

Category:Molecular dynamics software

Category:Molecular modelling software