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2. Comparison of software for molecular mechanics modeling

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

   Molecular building (DNA, proteins, hydrocarbons, nanotubes), molecular dynamics, GPU acceleration Mixed: free open source & commercial: Ascalaph Project: Avogadro: Yes Yes Yes No No No I No No Molecule building, editing (peptides, small molecules, crystals), conformational analysis, 2D/3D conversion; extensible interfaces to other tools

3. Spartan (chemistry software) - Wikipedia

   en.wikipedia.org/wiki/Spartan_(chemistry_software)

   Spartan is a molecular modelling and computational chemistry application from Wavefunction. [2] It contains code for molecular mechanics, semi-empirical methods, ab initio models, [3] density functional models, [4] post-Hartree–Fock models, [5] thermochemical recipes including G3(MP2) [6] and T1. [7], and machine learning models like ...

4. List of software for nanostructures modeling - Wikipedia

   en.wikipedia.org/wiki/List_of_software_for...

   Three dimensional molecular model of an all-carbon tubular fullerene. This is a list of notable computer programs that are used to model nanostructures at the levels of classical mechanics [1] and quantum mechanics. Furiousatoms [2] - a powerful software for molecular modelling and visualization; Aionics.io [3] - a powerful platform for ...

5. Coot (software) - Wikipedia

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

   Coot is free software, distributed under the GNU GPL. It is available from the Coot web site [4] originally at the University of York, and now at the MRC Laboratory of Molecular Biology. Pre-compiled binaries are also available for Linux and Windows from the web page and CCP4, and for Mac OS X through Fink and CCP4. Additional support is ...

6. MODELLER - Wikipedia

   en.wikipedia.org/wiki/MODELLER

   Modeller, often stylized as MODELLER, is a computer program used for homology modeling to produce models of protein tertiary structures and quaternary structures (rarer). [2] [3] It implements a method inspired by nuclear magnetic resonance spectroscopy of proteins (protein NMR), termed satisfaction of spatial restraints, by which a set of geometrical criteria are used to create a probability ...

7. List of protein structure prediction software - Wikipedia

   en.wikipedia.org/wiki/List_of_protein_structure...

   Constituent amino-acids can be analyzed to predict secondary, tertiary and quaternary protein structure. This list of protein structure prediction software summarizes notable used software tools in protein structure prediction, including homology modeling, protein threading, ab initio methods, secondary structure prediction, and transmembrane helix and signal peptide prediction.