Molecular Science Software

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Molecular Science Software

  • Focus on your Business with an integrated Business Cloud Focus on your Business with an integrated Business Cloud Icon
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  • RasMol

    The SourceForge OpenRasMol project is an adjunct to the RasMol and OpenrasMol project at http://rasmol.org. It is hoped that the SourceForge OpenRasMol project will provide a convenient focal point for active collaborative contributions.

  • ProteoConnections Icon

    ProteoConnections

    ProteoConnections is a bioinformatics platform tailored to address the pressing needs of proteomic analyses. Organise identifications, evaluate the the acquired dataset and accelerate biological interpretation using bioinformatics applications.

  • ProtPOS Icon

    ProtPOS

    Prediction of PROTtein Preferred Orientation on a Surface

    ProtPOS is a self-contained, lightweight, and easy-to-use software package for predicting the preferred orientation of protein on a given surface upon initial adsorption. It searches quickly for the low energy protein poses in all translational and rotational degrees of freedom of the protein with respect to the surface using particle swarm optimization. Each successful run returns the lowest energy orientation of the protein on the surface in PDB format, which is readily used for MD simulations. ProtPOS is implemented in Python, making use of the PyMOL library for generating protein conformations and calling GROMACS externally to calculate protein-surface interaction energies.

    Downloads: 0 This Week Last Update: See Project
  • the little b modular modeling language

    Little b is a Lisp-based language which allows scientists to build shareable, reusable mathematical models of complex systems based on shared parts. The initial focus is molecular and multicellular networks. Project web page: http://www.littleb.org

    Downloads: 0 This Week Last Update: See Project
  • GEMS

    Grid-Enabled Molecular Simulation Repository (GEMS)

    Downloads: 0 This Week Last Update: See Project
  • sassie

    Use SASSIE to generate and manipulate large numbers of molecular structures and then calculate the SAXS, SANS, and neutron reflectivity profiles from atomistic structures. Use for intrinsically disordered proteins. We need alpha-testers and developers.

    Downloads: 0 This Week Last Update: See Project
  • Xwalk

    Xwalk calculates a “Solvent Accessible Surface Distance”, which corresponds to the length of the shortest path between two protein atoms, where the path leads through solvent occupied space without penetrating the protein surface.

    Downloads: 0 This Week Last Update: See Project
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