Innovative Structural Biology

Software

Find_XL
[DOWNLOAD]
A software package that identifies cross-links in mass-spectrometry data. The package comes with detailed documentation and a working example from cross-linked sample of RNA polymerase II. The code is written in MATLAB and you need to run it in the MATLAB environment.

If you use 'Find_XL' in a publication, please cite:

Kalisman N, Adams CM, Levitt M. Subunit order of eukaryotic TRiC/CCT chaperonin by cross-linking, mass spectrometry, and combinatorial homology modeling. PNAS, 109:2884-9, 2012.
Automatic Sequence Inference (Crystallography)
[INSTALLER] [README]
A software package that, given the crystallographic structure factors and a backbone trace, automatically identifies the type of amino acid at any position along the backbone. Very good results were shown for low-reolution crystallographic datasets of up to 4 Angs. This package only runs on UNIX machines.

If you use the Automatic Sequence Inference Software in a publication, please cite:

Ben-Aharon Z, Levitt M, Kalisman N. Automatic inference of sequence from low-resolution crystallographic data. Under Review, 2017.