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Saric M. "Free Molecular Modelling Programs =". A rather detailed, objective, and technical assessment of about 20 tools. "PDB list of molecular graphics tools". "Index of Molecular Visualization Resources". "Molecular Visualization Resources by Eric Martz"
Avogadro is a molecule editor and visualizer designed for cross-platform use in computational ... interactive tools, commands, ... List of molecular graphics systems;
Software tools for molecular design-Tinker-OpenMM [6] Software tools for molecular design-Tinker-HP [7] Proprietary, gratis Washington University: UCSF Chimera: Yes Yes Yes No No No No No No Visually appealing viewer, amino acid rotamers and other building, includes Antechamber and MMTK, Ambertools plugins in development. Proprietary, free ...
Avogadro: C++ based molecule editor and visualizer for in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. Linux, macOS, Unix, Windows: 3-Clause BSD License: Open Chemistry Project: BEDtools "Genome arithmetic"—manipulation of coordinate sets and the extraction of sequences from a BED file ...
They may also include density functional theory (DFT), molecular mechanics or semi-empirical quantum chemistry methods. The programs include both open source and commercial software. Most of them are large, often containing several separate programs, and have been developed over many years.
Download as PDF; Printable version; ... Avogadro (software) B. ... List of software for Monte Carlo molecular modeling; List of software for nanostructures modeling; M.
The fourth is a great example of how interactive graphical tools enable a worker involved in sequence analysis to conveniently execute a variety if different computational tools to explore an alignment's phylogenetic implications; or, to predict the structure and functional properties of a specific sequence, e.g., comparative modelling.
Via chamber tool since v11 Yes No No No Ascalaph Designer: UA 94, 99SB, 03 No No No No No Avogadro: No No No Yes 94, 94s No Yes Balloon: No No No No 94 No No MMFF94-like BOSS: Yes No No No No No No CHARMM: Yes* Yes* Yes* Via CHARMM-GUI [2] Full MMFF94, but code rumored unmaintained No No * in standard distribution Gabedit: No Yes No Yes Yes No No