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Automatic building of protein atomic models from cryo-EM density maps using residue co-evolution
| dc.rights.license | open | en_US |
| dc.contributor.author | BARDIAUX, Benjamin | |
| dc.contributor.author | PELLARIN, Riccardo | |
| hal.structure.identifier | Microbiologie Fondamentale et Pathogénicité [MFP] | |
| dc.contributor.author | RAPISARDA, Chiara | |
| dc.contributor.author | NILGES, Michael | |
| dc.date.accessioned | 2023-05-31T14:57:48Z | |
| dc.date.available | 2023-05-31T14:57:48Z | |
| dc.date.created | 2020-01 | |
| dc.identifier.uri | https://oskar-bordeaux.fr/handle/20.500.12278/182398 | |
| dc.description.abstractEn | Electron cryo-microscopy (cryo-EM) has emerged as a powerful method to obtain three-dimensional (3D) structures of macromolecular complexes at atomic or near-atomic resolution. However, de novo building of atomic models from near-atomic resolution (3-5 Å) cryo-EM density maps is a challenging task, in particular since poorly resolved side-chain densities hamper sequence assignment by automatic procedures at a lower resolution. Furthermore, segmentation of EM density maps into individual subunits remains a difficult problem when no three-dimensional structures of these subunits exist, or when significant conformational changes occur between the isolated and complexed form of the subunits. To tackle these issues, we have developed a graph-based method to thread most of the C- α trace of the protein backbone into the EM density map. The EM density is described as a weighted graph such that the resulting minimum spanning tree encompasses the high-density regions of the map. A pruning algorithm cleans the tree and finds the most probable positions of the C- α atoms, using side-chain density when available, as a collection of C- α trace fragments. By complementing experimental EM maps with contact predictions from sequence co-evolutionary information, we demonstrate that our approach can correctly segment EM maps into individual subunits and assign amino acids sequence to backbone traces to generate full-atom models. | |
| dc.language.iso | EN | en_US |
| dc.rights.uri | http://creativecommons.org/licenses/by-nc-nd/ | |
| dc.title.en | Automatic building of protein atomic models from cryo-EM density maps using residue co-evolution | |
| dc.type | Document de travail - Pré-publication | en_US |
| dc.identifier.doi | 10.1101/2020.01.03.893669 | en_US |
| dc.subject.hal | Sciences du Vivant [q-bio]/Biochimie, Biologie Moléculaire/Biophysique | en_US |
| dc.subject.hal | Sciences du Vivant [q-bio]/Biochimie, Biologie Moléculaire/Biologie moléculaire | en_US |
| bordeaux.hal.laboratories | MFP (Laboratoire Microbiologie Fondamentale et Pathogénicité) - UMR 5234 | en_US |
| bordeaux.institution | CNRS | en_US |
| bordeaux.import.source | hal | |
| hal.identifier | pasteur-03063879 | |
| hal.version | 1 | |
| hal.export | false | |
| workflow.import.source | hal | |
| dc.rights.cc | Pas de Licence CC | en_US |
| bordeaux.COinS | ctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.au=BARDIAUX,%20Benjamin&PELLARIN,%20Riccardo&RAPISARDA,%20Chiara&NILGES,%20Michael&rft.genre=preprint |
