Data to reproduce the EMMIVox model refinement benchmark described in:
S. E. Hoff, F. E. Thomasen, K. Lindorff-Larsen, M. Bonomi. Accurate model and ensemble refinement using cryo-electron microscopy maps and Bayesian inference. bioRxiv 2023 doi: 10.1101/2023.10.18.562710.
Details about the systems used in our benchmark are reported in the table below. Instructions to install GROMACS and PLUMED as well as analysis scripts and complete tutorials can be found here.
Details of the benchmark systems
| ID | PDB ID | EMDB ID | resolution [Å] | # protein residues | # protein chains | # waters | # lipids | # ligands | # waters | # lipids | # buffer ions | # atoms |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 01 | 7p6a | 13223 | 1.90 | 540 | 5 | 76 | 0 | 0 | 10,782 | 0 | 124 | 40,805 |
| 02 | 7w9w | 32377 | 2.02 | 810 | 3 | 144 | 24 | 0 | 17,548 | 169 | 113 | 86,452 |
| 03 | 7n00 | 24095 | 2.27 | 806 | 2 | 0 | 0 | 0 | 43,754 | 0 | 260 | 143,124 |
| 04 | 7t4n | 25681 | 2.35 | 914 | 2 | 0 | 0 | 0 | 100,987 | 0 | 574 | 318,262 |
| 05 | 7b5o | 12042 | 2.50 | 651 | 3 | 73 | 0 | 1 | 50,944 | 0 | 289 | 163,693 |
| 06 | 7mjs | 23883 | 3.03 | 715 | 3 | 0 | 1 | 2 | 29,943 | 190 | 168 | 126,588 |
| 07 | 7lq6 | 23482 | 3.28 | 717 | 1 | 0 | 0 | 0 | 80,921 | 0 | 465 | 254,485 |
| 08 | 7nqk | 12528 | 3.50 | 781 | 2 | 0 | 0 | 0 | 39,764 | 328 | 222 | 175,791 |
| 09 | 6yeg | 10792 | 4.00 | 2064 | 12 | 0 | 0 | 0 | 60,592 | 0 | 496 | 212,980 |
Model validation
To validate the deposited PDBs and the EMMIVox single-structure model using the metrics described in the manuscript, please:
- download the analysis scripts here;
- download the PDB structures and cryo-EM maps using the script
get_PDB_MAP.sh; - run the validation of the deposited PDBs with
validate_PDB.sh; - run the validation of the EMMIVox models with
validate_EMMIVox.sh.
Contact
For any technical questions, please write to mbonomi_at_pasteur.fr.