List of Tans

  • Calculation setup

    • MMSetup: Setup MD calculations with OpenMM and ommprotocol [WIP]
    • QMSetup: QM and QM/MM calculations setup
  • Visualization

    • 3D-SNFG: Enable easy visualization of saccharydic residues
    • BondOrder: Automatic bond order perception for UCSF Chimera [WIP]
    • GAUDIView: Lightweight visualization of results coming from docking, conformational search or multiobjective optimization
    • TalaDraw: Build 3D structures out of two-dimensional sketches
  • Analysis

    • NCIPlotGUI: Straightforward interface to setup calculations for NCIPlot and visualize them
    • NormalModes: Perform Normal Modes Analysis and view them directly on-screen
    • PLIPGUI: Depict protein-ligand interactions, as calculated with PLIP
    • PoPMuSiCGUI: Depict and apply the predictions made by PoPMuSiC calculations
    • PropKaGUI: Analyze and depict the expected pKa values of protein residues with PropKa 3.1
    • SubAlign: Align two, potentially different, molecules based on partial matches of substructures
  • Utilities & Patches

    • DummyMetal: A subtle modification to UCSF Chimera’s MetalGeom extension to allow arbitrary elements to be placed at vacant positions, instead of just oxygens
    • OrbiTraj: A subtle modification to UCSF Chimera’s MD Movie extension to allow the visualization of volumetric data along a molecular trajectory
    • ReVina: Resubmit failed AutoDock Vina jobs without reconfiguring the GUI