Molecular design software

Summary

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

  • 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 SN Website Comments
Abalone Yes Yes Yes Yes Yes Yes Yes Yes No Yes Yes Yes Yes No biomolecular-modeling.com Biomolecular graphics environment: macromolecule builders, GPU accelerated MD
AMBER No No No Yes Yes No No Yes No Yes Yes No Yes No Yes ambermd.org Classical molecular modeling program
Ascalaph Designer Yes Yes Yes Yes Yes Yes Yes Yes No Yes Yes Yes Yes No Agile Molecule Common molecular modeling suite
BOSS No No No No No No No Yes No Yes Yes Yes Yes No Yale University OPLS inventor
Discovery Studio Yes Yes Yes Yes Yes Yes Yes Yes Yes Yes Yes Yes Yes Yes Dassault Systèmes BIOVIA 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 University of California DOCK algorithm
Firefly (PC GAMESS) No No No No No No No Yes No Yes No Yes Yes No Moscow State University Ab initio and DFT computational chemistry program
FoldX No No No No No No No Yes No Yes Yes No Yes No CRG 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 MolTech Molecular docking package
Materials Studio Yes Yes Yes No No Yes Yes Yes Yes Yes Yes Yes Yes No Dassault Systèmes BIOVIA Software environment
Molecular Operating Environment (MOE) Yes Yes Yes Yes Yes Yes Yes Yes Yes Yes Yes Yes Yes Yes Yes Chemical Computing Group 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 RosettaCommons 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 SAMSON Connect 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 Fujitsu General purpose molecular modeling suite
Spartan Yes Yes No Yes Yes No Yes Yes No Yes Yes Yes No No Wavefunction 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 Washington University Tools for protein design; freeware
Winmostar Yes Yes Yes No No Yes Yes Yes No Yes Yes Yes Yes No X-Ability Molecular modeling and visualizing program for materials science

Notes and references

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.
  • Journal of Chemical Information and Modeling
  • Journal of Computational Chemistry