AlphaPulldown

A Python package that streamlines protein-protein interaction screens and high-throughput modelling of higher-order oligomers using AlphaFold-Multimer

Assembline

Pipeline for integrative structural modeling of macromolecular complexes

ColabSeg

An interactive tool for editing, processing, and visualizing membrane segmentations from cryo-ET data

PyTME

The programming library and software for template matching on electron microscopy data.

Xlink Analyzer

An interactive software for visualising cross-links on structures and analysing how the structures agree with the cross-links.

Relax

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.

efitter

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!

Fitter

Code for fast EM fitting and more.

pdb_utils

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.

pyxlinks

A Python package for dealing with cross-linking/MS data. Used by Xlink Analyzer but can be used standalone too.

modeling_utils

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.

It is quite a ground-braking script because it features:

• oligomeric/multi-chain modeling and multiple templates
• optional removal of tails and inserts
• and keeping the correct residue numbering with the above
• setting unique chain ids to the output chains
• provides command line options for controlling optimization levels and number of output models

A useful programming library is also included.

alphafold_howto

Collection of SLURM script examples for running AlphaFold and RoseTTAFold. Adjusted to EMBL compute cluster but could work for you too with some adjustments.