Molecular design software

Molecular design software is 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
CULGI Yes Yes Yes Yes Yes Yes Yes Yes No Yes Yes Yes Yes Yes CULGI CULGI experts in automated coarse-grained mulstiscale modeling, construction of complex materials
Bench (Cyrus Biotechnology) Yes No Yes Yes Yes Yes No Yes No Yes No No No No Cyrus Biotechnology A graphical version of Rosetta with associated tools running on the cloud. Protein design, protein/ligand interface, protein/protein interface affinity and specificity, protein stability design, protein/antibody structure prediction.
ChemDoodle 3D (iChemLabs) Yes Yes No No No No No Yes No Yes Yes No No No ChemDoodle 3D Intuitive building of molecules in real-time; production of high quality publication graphics; works on Windows, macOS and Linux; developed by iChemLabs
DENEB Yes Yes Yes Yes Yes Yes Yes No No Yes No Yes No No Atelgraphics Atom-scale modeling software for full cycle design, calculation, and analysis; interfaces with DFT engines
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
Forecaster and Virtual Chemist Yes Yes No No No No No Yes Yes Yes Yes No Yes No Molecular Forecaster Inc. The FORECASTER and VIRTUAL CHEMIST platforms are collections of proprietary program for drug design and discovery (FORECASTER) and for virtual organic chemistry (VIRTUAL CHEMIST). The automation and modularity support a variety of experiments.
HyperChem with HMHC and DSHC Yes Yes Yes Yes Yes Yes Yes Yes Yes Yes Yes Yes Yes Yes Hypercube, Inc. and Motonori Tsuji A Sophisticated Molecular Modeling Environment
Lead Finder No No No No No No No Yes Yes No Yes No No No MolTech Molecular docking package
LigandScout (Inte:Ligand) Yes Yes Yes Yes Yes Yes Yes Yes Yes Yes Yes No No No LigandScout Advanced molecular modelling, virtual screening and drug design software
Maestro (Schrödinger) Yes Yes Yes Yes Yes Yes Yes Yes Yes Yes Yes Yes Yes Yes Yes Yes Schrodinger Molecular modeling and visualizing program for drug design and materials science
MAPS Yes Yes Yes No Yes Yes Yes Yes Yes Yes Yes Yes Yes Yes Scienomics Multi-scale, multi-paradigm, extensible platform that allows to build, simulate and analyze complex materials.
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
SeeSAR Yes Yes No No Yes No Yes No Yes Yes Yes No No Yes Yes Yes Yes BioSolveIT: SeeSAR, infiniSee, etc. Structure-based design in 3D, visual and interactive Molecular Modeling / drug discovery, ligand design and docking, Space Navigation
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
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