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The Info List - Molecular Design Software


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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:

Molecular graphics interactive molecular drawing and conformational editing building polymeric molecules, crystals, and solvated systems partial charges development geometry optimization support for the different aspects of force field development

Contents

1 Comparison of software covering the major aspects of molecular design 2 Notes and references 3 See also 4 External links

Comparison of software covering the major aspects of molecular design[edit]

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

3D Mouse Poly DNA Pept Cryst Solv Q Dock Min MM QM FF QSAR 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 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

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 any 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 Schrodinger Molecular modeling
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
Molecular Operating Environment
(MOE) 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

SAMSON Yes Yes No No No Yes No No Yes Yes Yes Yes Yes No SAMSON
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
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
Molecular modeling
and visualizing program for materials science

Notes and references[edit]

See also[edit]

Molecule editor Molecular modelling Molecular modeling
Molecular modeling
on GPUs Protein design Drug design Force field (chemistry) Comparison of force field implementations Comparison of nucleic acid simulation software Comparison of software for molecular mechanics modeling List of molecular graphics systems List of software for Monte Carlo molecular modeling List of software for nanostructures modeling Quantum chemistry computer programs Quantitative structure-activity relationship

External links[edit]

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)

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