{"id":50,"date":"2019-09-18T12:32:56","date_gmt":"2019-09-18T12:32:56","guid":{"rendered":"https:\/\/www.embl.org\/groups\/kosinski\/?page_id=50"},"modified":"2025-05-29T20:15:22","modified_gmt":"2025-05-29T20:15:22","slug":"software","status":"publish","type":"page","link":"https:\/\/www.embl.org\/groups\/kosinski\/software\/","title":{"rendered":"Software"},"content":{"rendered":"\n
\n

\n \n \n AlphaPulldown\n <\/a>\n <\/h3>\n\n

A Python package that streamlines protein-protein interaction screens and high-throughput modelling of higher-order oligomers using AlphaFold-Multimer<\/p>\n<\/article>\n\n\n\n

\n

\n \n \n Assembline\n <\/a>\n <\/h3>\n\n

Pipeline for integrative structural modeling of macromolecular complexes<\/p>\n<\/article>\n\n\n\n

\n

\n \n \n PyTME\n <\/a>\n <\/h3>\n\n

The programming library and software for template matching on electron microscopy data.<\/p>\n<\/article>\n\n\n\n

\n

\n \n \n HMFF and Mosaic\n <\/a>\n <\/h3>\n\n

Integrative modeling of biological membranes based on electron microscopy and other density data, membrane simulations, and membrane morphometrics<\/p>\n<\/article>\n\n\n\n

\n

\n \n \n AF3x\n <\/a>\n <\/h3>\n\n

Custom modification of AlphaFold 3 enabling explicit modeling of crosslinks<\/p>\n<\/article>\n\n\n\n

\n

\n \n \n ColabSeg\n <\/a>\n <\/h3>\n\n

An interactive tool for editing, processing, and visualizing membrane segmentations from cryo-ET data<\/p>\n<\/article>\n\n\n\n

\n

\n \n \n Xlink Analyzer\n <\/a>\n <\/h3>\n\n

An interactive software for visualising cross-links on structures and analysing how the structures agree with the cross-links.<\/p>\n<\/article>\n\n\n\n

Programming libraries and other packages<\/h2>\n\n\n\n

<\/p>\n\n\n\n

\n

\n \n \n Relax\n <\/a>\n <\/h3>\n\n

Scripts to minimize macromolecular structures, for example unrelaxed AlphaFold models. Producing nice PDB files, and keeping original chain IDs. Keeping the PDB in the original reference frame. Optionally resolving side chains threading rings of aromatic side chains.<\/p>\n<\/article>\n\n\n\n

\n

\n \n \n efitter\n <\/a>\n <\/h3>\n\n

A wrapper for running UCSF Chimera Fit in Map global search from command line plus statistical analysis. This is the first step of Assembline pipeline but can be also used separately as an EM fitting program. Gives p-values for your fits!<\/p>\n<\/article>\n\n\n\n

\n

\n \n \n Fitter\n <\/a>\n <\/h3>\n\n

Code for fast EM fitting and more.<\/p>\n<\/article>\n\n\n\n

\n

\n \n \n pdb_utils\n <\/a>\n <\/h3>\n\n

Scripts for dealing with PDB files – renumber residues, rename chains, cut and merge PDB files and many others without modifying parts that do not need to be modified.<\/p>\n<\/article>\n\n\n\n

\n

\n \n \n pyxlinks\n <\/a>\n <\/h3>\n\n

A Python package for dealing with cross-linking\/MS data. Used by Xlink Analyzer but can be used standalone too.<\/p>\n<\/article>\n\n\n\n

\n

\n \n \n modeling_utils\n <\/a>\n <\/h3>\n\n

modeling_utils provide a modeling script that give a sequence alignment automates the most common tasks in homology modeling and provides utilities to prepare the input.<\/p>\n

It is quite a ground-braking script because it features:<\/p>\n