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ANR project: Code decision (reference) : ANR-19-CE11-0008
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Hybrid Electron Microscopy Normal Mode Analysis with Scipion

Mohamad Harastani , Carlos Oscar S. Sorzano , Slavica Jonic
Protein Science, 2020, 29 (1), pp.223-236. ⟨10.1002/pro.3772⟩
Journal articles hal-02388487v1
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DeepHEMNMA: ResNet-based hybrid analysis of continuous conformational heterogeneity in cryo-EM single particle images

Ilyes Hamitouche , Slavica Jonic
Frontiers in Molecular Biosciences, 2022, 9, pp.965645. ⟨10.3389/fmolb.2022.965645⟩
Journal articles hal-03750789v1
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NMMD: Efficient cryo-EM flexible fitting based on simultaneous Normal Mode and Molecular Dynamics atomic displacements

Rémi Vuillemot , Osamu Miyashita , Florence Tama , Isabelle Rouiller , Slavica Jonic et al.
Journal of Molecular Biology, 2022, 434 (7), pp.167483. ⟨10.1016/j.jmb.2022.167483⟩
Journal articles hal-03577246v1
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MDSPACE: Extracting continuous conformational landscapes from cryo-EM single particle datasets using 3D-to-2D flexible fitting based on Molecular Dynamics simulation

Rémi Vuillemot , Alex Mirzaei , Mohamad Harastani , Ilyes Hamitouche , Léo Fréchin et al.
Journal of Molecular Biology, 2023, pp.167951. ⟨10.1016/j.jmb.2023.167951⟩
Journal articles hal-03929029v1
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Combined Bayesian and Normal Mode Flexible Fitting with Hamiltonian Monte Carlo Sampling for Cryo Electron Microscopy

Rémi Vuillemot , Slavica Jonic
29th European Signal Processing Conference, EUSIPCO 2021, Aug 2021, Dublin, Ireland. pp.1211-1215, ⟨10.23919/EUSIPCO54536.2021.9616150⟩
Conference papers hal-03266628v1
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Deep learning of elastic 3D shapes for cryo electron microscopy analysis of continuous conformational changes of biomolecules

Ilyes Hamitouche , Slavica Jonic
29th European Signal Processing Conference, EUSIPCO 2021, Aug 2021, Dublin, Ireland. pp.1251-1255, ⟨10.23919/EUSIPCO54536.2021.9616013⟩
Conference papers hal-03266630v1
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Code and test data of ContinuousFlex plugin for analyzing continuous conformational variability of biomolecular complexes in cryo-EM and cryo-ET data

Slavica Jonic , Mohamad Harastani
Software hal-03501129v1
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ContinuousFlex: Software package for analyzing continuous conformational variability of macromolecules in cryo electron microscopy and tomography data

Mohamad Harastani , Rémi Vuillemot , Ilyes Hamitouche , Nima Barati Moghadam , Slavica Jonic et al.
Journal of Structural Biology, 2022, 214 (4), pp.107906. ⟨10.1016/j.jsb.2022.107906⟩
Journal articles hal-03821777v1