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Avogadro is a molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, ... interactive tools, commands, ...
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"
Suite of automated docking tools Linux, Mac OS X, SGI IRIX, and Windows: GPL: Scripps Research: 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
A notable molecule editor is a computer program for creating and modifying representations of chemical structures.. Molecule editors can manipulate chemical structure representations in either a simulated two-dimensional space or three-dimensional space, via 2D computer graphics or 3D computer graphics, respectively.
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.
High performance GPU-accelerated ab initio molecular dynamics and TD/DFT software package for very large molecular or even nanoscale systems. Runs on NVIDIA GPUs and 64-bit Linux, has heavily optimized CUDA code. Proprietary, trial licenses available PetaChem LLC: TINKER: I Yes Yes Yes Yes I I Yes Yes Software tools for molecular design-Tinker ...
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
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.