Innovative Structural Biology

Software

Inferring the mass of linker adducts
[README] [MATLAB package]
A MATLAB application (with GUI) that can infer the mass of cross-link adducts in mass spectrometry data of proteins. The package includes example files of data from DSS cross-linking. The paper describing this work is:

Slavin M, et al. Open search strategy for inferring the masses of cross-link adducts on proteins. Analytical Chemistry, under revision, 2020.
Search for formaldehyde cross-links
[README] [APPLICATION] [EXAMPLE_1] [EXAMPLE_2]
A stand-alone application to identify formaldehyde cross-links in mass spectrometry data. The application is intended to search against any sequence databases (up to 25,000 sequences). The inputs to the search are a FASTA file with the sequences and a MGF file with the mass spectrometry data. Two examples with corresponding input files are available:
Example 1 - Data from formaldehyde cross-linking of a mixture of three proteins.
Example 2 - Data from in situ formaldehyde cross-linking of human PC9 cells in culture.

We would like to get your feedback if you use it and find issues. The source code (in Java) is available upon request from Nir Kalisman. This application runs only on Windows machines.

Tayri-Wilk T, et al. Mass spectrometry reveals the chemistry of formaldehyde cross-linking in structured proteins. Nat Comm, 2020.
Automatic Sequence Inference (Crystallography)
[README] [INSTALLER] [SOURCE CODE]
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 4.5 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. Structure, 2018.
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.