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  2. List of molecular graphics systems - Wikipedia

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

    Build, edit and visualise small molecules, macromolecules, protein-ligand complexes, crystal lattices, molecular and property surfaces. Platform for extensive collection of molecular modelling / drug discovery applications. Molekel: MM XRD: Free open-source: Java 3D applet or standalone program: Ovito: MM XRD EM MD: Free open-source: Python [13 ...

  3. 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.

  4. Comparison of software for molecular mechanics modeling

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

    Comprehensive life science modeling and simulation suite of applications focused on optimizing drug discovery process: small molecule simulations, QM-MM, pharmacophore modeling, QSAR, protein-ligand docking, protein homology modeling, sequence analysis, protein-protein docking, antibody modeling, etc. Proprietary, trial available

  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.

  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. Visual Molecular Dynamics - Wikipedia

    en.wikipedia.org/wiki/Visual_Molecular_Dynamics

    Molecular scenes can be exported to external rendering tools such as POV-Ray, RenderMan, Tachyon, Virtual Reality Modeling Language , and many others. Users can run their own Tcl and Python scripts within VMD as it includes embedded Tcl and Python interpreters. VMD runs on Unix, Apple Mac macOS, and Microsoft Windows. [3]

  8. UCSF Chimera - Wikipedia

    en.wikipedia.org/wiki/UCSF_Chimera

    UCSF Chimera (or simply Chimera) is an extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. [1]

  9. List of mass spectrometry software - Wikipedia

    en.wikipedia.org/wiki/List_of_mass_spectrometry...

    Software for mass spectrometry imaging designed to normalize, validate and interpret MS images. multiMS-toolbox Open source: MS-alone and multiMS-toolbox is a tool chain for mass spectrometry data peak extraction and statistical analysis. mzCloud Website

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