The modeling.py script demonstrates the use of IMP and PMI in the modeling of the 26S proteasome - UBLCP1 complex, using chemical crosslinking and comparative modeling.

The modeling protocol will work with a default build of IMP.

• modeling.py the main IMP/PMI script for modeling

• inputs

  • h26s_flex_fix.pdb comparative model of the 26S proteasome structure
  • ublcp1_t1_1.pdb comparative model of the UBLCP1 structure with its Ubl domain bound to T1 site
  • ublcp1_t1_2.pdb comparative model of the UBLCP1 structure with its Ubl domain bound to T2 site
  • sequences.fasta FASTA file with all the protein sequences
  • topology.txt IMP/PMI topology input file
  • xlinks.txt list of cross-links

• output An example IMP/PMI output directory obtained by running the modeling.py script

• python modeling.py

Author(s): Peter Cimermancic, Charles Greenberg

Date: May 17th, 2016

License: CC-BY-SA-4.0. This work is freely available under the terms of the Creative Commons Attribution-ShareAlike 4.0 International License.

Last known good IMP version:

Publications:

• X. Wang, P. Cimermancic, C. Yu, E. Sakata, X. Guo, C. Greenberg, A. Schweitzer, A.S. Huszagh, Y. Yang, E.J. Novitsky, A. Leitner, P. Nanni, A. Kahraman, J. Dixon, S.D. Rychnovsky, R. Aebersold, W. Baumeister, A. Sali, L. Huang. Molecular Details Underlying Dynamic Structures and Regulation of the Human 26S Proteasome, Mol Cell Proteomics 16(5):840-854, 2017