It:software-2011

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Software for CIT

This is a non-exhaustive list of software, including software that you will find on cluster PCs and other software available for you to install and use on your own computer. If there is anything you find useful, please add it to the list in the appropriate area, along with a brief description of what it does. If you find anything which is so useful you think it should be installed on the cluster computers, please do speak to either Professor Henry Rzepa or Dr. Andrew McKinley and we can investigate any possibilities.

Software listed by category

Spectroscopic software

• gNMR5 - NMR simulation software
• Mestrenova - NMR spectral analysis software
• mMass - Mass spectrometry software
• Spinworks 3 - NMR analysis software
• Torganal - Spectroscopic training software

Molecular visualisation software

• Avogadro - visualiser, multiplatform
• Gaussview - viewer for Gaussian output
• Mercury 2.3 - CCDC visualisation application
• PyMOL tools - Molecular visualization system on an open-source foundation
• VMD - Software for visualisation
• wxMacMolPlt - Simple molecular display, visualisation of symmetries
• Accelrys - Visualisation software
  • Discovery Studio Visualiser
  • DS Visualiser
  • Accelrys Viewer lite
• Hermes - Comprehensive Protein Visualiser
• ChemBio3D Ultra - Molecular graphics and computational methods package
• VMD - Visual Molecular Dynamics - for analysing large biomolecular systems

Data mining software

• Conquest - Search the Cambridge Structural Database (CSD)
• IsoStar Client - A Knowledge Base of Intermolecular Interactions
• Mogul - A Knowledge Base of Molecular Geometry
• Prequest - Creation of In-House Databases in CSD format
• ChemBioFinder Std - A chemically and biologically intelligent database manager and search engine
• Scifinder Scholar - Client software for SciFinder; redundant as of 2011

Drawing packages

• ChemBioOffice 2010
  • ChemBio3D Ultra - Molecular graphics and computational methods package
  • ChemDraw Pro - Chemical structure drawing and more
• DeLano Scientific
• Gimp - The GNU Image Manipulation Program

Computational Chemistry Packages

• Gold - program for calculating the docking modes of small molecules in protein binding sites
• SuperStar - Predicting Protein-Ligand Interactions Using Experimental Data
• Gabedit - A graphical user interface for computational chemistry packages

• Gaussian 03W - Electronic structure modelling
• Gaussian 09W - Electronic structure modelling
• GaussView 5.0 - Visualisation of Gaussian output
• MATLAB - Mathematical modelling and data analysis
• OpenBabel - Toolbox to use different languages of chemistry data
• VMD - Visual Molecular Dynamics - for analysing large biomolecular systems

Data Analysis software

• GnuPlot - Graphing utility
• MATLAB - Mathematical modelling and data analysis
• OriginLab - Data analysis and graphing software

Education and learning software

• Torganal2 - Spectroscopy training software

Report writing tools

• GnuPlot - Graphing utility
• Microsoft Office
• OpenOffice - Free alternative to Microsoft Office

Citation and document library software

• Mendeley desktop - document library manager
• Endnote - Citation management software
• Refworks - Citation management - Free for IC students

Utilities

• Adobe Reader 9 - PDF reader
• PuTTy - command line TelNet SSH tool
• XPS viewer - Tool for viewing XML files
• Filezilla FTP - Free FTP software

• Google Earth
• iTunes
• jDiskReport - Monitor hard disk space usage
• Mozilla Firefox - Extensible web browser
• OpenBabel - Toolbox to use different languages of chemistry data
• PrimoPDF - Free PDF virtual printing software
• Quicktime
• RealPlayer
• Winzip
• Xming - X Window server for Windows

Software installed on Chemistry Cluster Computers

Start menu items

• Adobe Reader 9 - PDF reader
• Avogadro - visualiser, multiplatform
• Conquest - accessing Cambridge Structure DataBase
• Gaussian 03 - Molecular modelling
• Gaussian 09 - Molecular modelling
  • Gaussview - viewer for Gaussian output
• gNMR5 - NMR simulation software
• Mendeley desktop - document library manager
• Mercury 2.3 - CCDC visualisation application
• Mestrenova - NMR spectral analysis software
• mMass - Mass spectrometry software
• PuTTy - command line TelNet SSH tool
• PyMOL - Molecular graphics software
• Spinworks 3 - NMR analysis software
• Torganal - Spectroscopic training software
• VMD - Software for visualisation
• wxMacMolPlt - Simple molecular display, visualisation of symmetries
• XPS viewer - Tool for viewing XML files

Start menu folders

• Accelrys - Visualisation software
  • Discovery Studio Visualiser
  • DS Visualiser
  • Accelrys Viewer lite
• CCDC - Software from the Cambridge Crystallographic Data Centre
  • CSD System Software -> Mercury
  • CSD System Software 2011
    • Conquest - Search the Cambridge Structural Database (CSD)
    • IsoStar Client - A Knowledge Base of Intermolecular Interactions
    • Mercury - Crystal Structure Visualisation
    • Mogul - A Knowledge Base of Molecular Geometry
    • Prequest - Creation of In-House Databases in CSD format
  • Gold Suite
    • Gold - program for calculating the docking modes of small molecules in protein binding sites
    • Hermes - Comprehensive Protein Visualiser
  • SuperStar - Predicting Protein-Ligand Interactions Using Experimental Data
• ChemBioOffice 2010
  • ChemBio3D Ultra - Molecular graphics and computational methods package
  • ChemBioFinder Std - A chemically and biologically intelligent database manager and search engine
  • ChemDraw Pro - Chemical structure drawing and more
• DeLano Scientific
  • PyMOL tools - Molecular visualization system on an open-source foundation
• Endnote - Citation managment software
• Filezilla FTP - Free FTP software
• Gabedit - A graphical user interface for computational chemistry packages
• Gaussian 03W - Electronic structure modelling
• Gaussian 09W - Electronic structure modelling
• GaussView 5.0 - Visualisation of Gaussian output
• Gimp - The GNU Image Manipulation Program
• GnuPlot - Graphing utility
• Google Earth
• iTunes
• jDiskReport - Monitor hard disk space usage
• MATLAB - Mathematical modelling and data analysis
• Microsoft Office
• Mozilla Firefox - Extensible web browser
• OpenBabel - Toolbox to use different languages of chemistry data
• OpenOffice - Free alternative to Microsoft Office
• OriginLab - Data analysis and graphing software
• PrimoPDF - Free PDF virtual printing software
• Quicktime
• RealPlayer
• Refworks - Citation management - Free for IC students
• Scifinder Scholar - Client software for SciFinder; redundant as of 2011
• Torganal2 - Spectroscopy training software
• University of Illinois
  • VMD - Visual Molecular Dynamics - for analysing large biomolecular systems
• Winzip
• Xming - X Window server for Windows

Software licensing

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