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  2. Avogadro (software) - Wikipedia

    en.wikipedia.org/wiki/Avogadro_(software)

    Avogadro is a molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, ...

  3. List of molecular graphics systems - Wikipedia

    en.wikipedia.org/wiki/List_of_molecular_graphics...

    Graphics, model building, molecular mechanics, quantum chemistry. Avizo: EM MM MRI Optical SMI XRD: Proprietary [5] Windows, Linux, Mac [6] [self-published source?] Avizo is derived from Amira and focusing on materials science. Avogadro: MM XRD MD: Free open-source, GPL C++, Qt, extensible via Python modules BALL: Molecular dynamics MM NMR ...

  4. List of open-source bioinformatics software - Wikipedia

    en.wikipedia.org/wiki/List_of_open-source...

    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 ...

  5. Molecule editor - Wikipedia

    en.wikipedia.org/wiki/Molecule_editor

    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.

  6. Comparison of software for molecular mechanics modeling

    en.wikipedia.org/wiki/Comparison_of_software_for...

    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 ...

  7. List of quantum chemistry and solid-state physics software

    en.wikipedia.org/wiki/List_of_quantum_chemistry...

    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.

  8. Extended Hückel method - Wikipedia

    en.wikipedia.org/wiki/Extended_Hückel_method

    A program for the extended Hückel method is YAeHMOP which stands for "yet another extended Hückel molecular orbital package". [10] YAeHMOP has also been merged with the Avogadro open-source molecular editor and visualizer to enable calculations directly from the Avogadro graphical user interface for materials that are periodic in one, two, or ...

  9. List of alignment visualization software - Wikipedia

    en.wikipedia.org/wiki/List_of_alignment...

    DNASTAR Lasergene Molecular Biology Suite Yes Yes Yes Align DNA, RNA, protein, or DNA + protein sequences via a variety of pairwise and multiple sequence alignment algorithms, generate phylogenetic trees to predict evolutionary relationships, explore sequence tracks to view GC content, gap fraction, sequence logos, translation