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Internals - Analysis tools


    SAP (Spatial-Aggregation-Propensity) algorithm predicts the aggregation prone regions of a protein:

    N. Chennamsetty et al., PNAS, 106, 11937 (2009)

    The main scripts and an example run can be downloaded here.

    Click here for a short introduction and the relative documentation.

Chirality Index

    The Chirality Index algorithm calculates the local backbone chirality of proteins:

    A. Pietropaolo et al., Proteins, 70, 667 (2008)

    and nucleic acids

    A. Pietropaolo and M. Parrinello, Chirality, 23, 534 (2011).

    The procedure calculates the chirality indexes for the backbone coordinates for a static Xray structure, as well as the average chirality indexes for multiple pdb structures, as an NMR model. A different code to treat MD trajectories calculates the evolution of the chirality indexes along the trajectory, as well the average chirality indexes for the backbone coordinates.

    The two fortran codes, instructions and an example input and output file can be downloaded here.