This repository contains a benchmark of hetero-dimeric complexes, with component atomic structures and chemical crosslinks. It is used to compare integrative modeling methods: EASAL and IMP.
There are 40 cases in benchmark, varying in crosslinker type, number of crosslinks, source of crosslinks, false positive rate, and source of monomer structures of the constituent proteins. The benchmark cases are divided based on the source of crosslinks in benchmark directory. Refer to the benchmark/simulated/README.md and benchmark/experimental/README.md for details. False positve simulated DSSO crosslinks were manually selected.
See installation_and_running.md for instructions for installing and running IMP and EASAL
The model ensembles obtained from IMP and EASAL are compared based on fit to the input crosslinks, similarity with the native structure, and efficiency. See scripts/compare_ensembles/ for the scripts to compare the results from IMP and EASAL.
Author(s): Yichi Zhang, Muskaan Jindal, Shruthi Viswanath, Meera Sitharam
License: CC BY-SA 4.0
This work is licensed under the Creative Commons Attribution-ShareAlike 4.0
International License.
Publications: Zhang, Y., et. al. A new discrete-geometry approach for integrative docking of proteins using chemical crosslinks.