Links to useful software packages developed by EUTOPIA members

  • Kymoknot a webserver and software package to localize knots on polymers and analyze their dynamics. [link][webserver][article][github]
  • PyLink a PyMOL plugin to identify links between protein chains. [link][article]
  • PyLasso a PyMOL plugin to identify lassos [link][article]
  • KnotProt 2.0 database which collects information about proteins with knots, slipknots and knotoids based on X-ray, NMR, and Cryo-EM deposition [link][article]
  • LassoProt a server and database of proteins with lassos [link][article]
  • LinkProt a database of proteins with topological links [link][article]
  • Topoly a Python package that collects programs useful for polymer topology analysis [link]
  • AlphaKnot a server to measure entanglement in AlphaFold-solved protein models while considering pLDDT confidence values [link][article]
  • Nemaktis an open-source platform for propagating and visualising optical fields in complex birefringent media such as liquid crystal (LC) layers [link]
  • PDBe-KB collaboratively defining the biological context of structural data [article]

Github Repositories

  • Ring-o-rings python package to setup LAMMPS simulations of circular catenanes and analyze their results [link]
  • TAPLab GitLab. A repository of codes to simulate “Topologically Active Polymers” [link]
  • KnotPull reduces a user provided 3D structure, to simplify it, while preserving the topology of the chain [link]
  • Topostats a python toolkit for automated editing and analysis of Atomic Force Microscopy images. [link]
  • Superstructure. A repository to analyse hierarchical clustering in datasets [link]
  • Machine Learning knots. A repository with python code to run deep learning on datasets of knotted polymers [link]
  • kDNA AFM. A repository to run AFM-steered MD simulations to reconstruct the topology of linked structures [link]