Yasaman Karami

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Publications

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Stoichiometric insights into SARS-CoV-2 spike–ACE2 binding across variants

Ishola Abeeb Akinwumi , Sneha Bheemireddy , Laurent Chaloin , Serge Pérez , Hamed Khakzad et al.

Computational and Structural Biotechnology Journal, 2025, 27, pp.3285-3291. ⟨10.1016/j.csbj.2025.07.034⟩

Article dans une revue hal-05236496v1
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B3GALT6 mutations lead to compromised connective tissue biomechanics in Ehlers-Danlos syndrome

Roméo Milan Diana , Benjamin Jolivet , Jean-Baptiste Vincourt , Sébastien Hergalant , Grégory Francius et al.

JCI Insight, 2025, 10 (16), pp.e179474. ⟨10.1172/jci.insight.179474⟩

Article dans une revue hal-05234907v1
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Subtle Changes at the RBD/hACE2 Interface During SARS-CoV-2 Variant Evolution: A Molecular Dynamics Study

Aria Gheeraert , Vincent Leroux , Dominique Mias-Lucquin , Yasaman Karami , Laurent Vuillon et al.

Biomolecules, 2025, 15 (4), pp.541. ⟨10.3390/biom15040541⟩

Article dans une revue hal-05041555v1
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DynaRepo: the repository of macromolecular conformational dynamics

Omid Mokhtari , Emmanuelle Bignon , Hamed Khakzad , Yasaman Karami

Nucleic Acids Research, 2025, pp.gkaf1130. ⟨10.1093/nar/gkaf1130⟩

Article dans une revue hal-05404177v1

Communication pathway analysis within protein-nucleic acid complexes

Sneha Bheemireddy , Roy González-Alemán , Emmanuelle Bignon , Yasaman Karami

Journal of Chemical Theory and Computation, 2025, 21 (17), pp.8255-8266. ⟨10.1101/2025.02.14.638259⟩

Article dans une revue hal-05041556v1
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Cysteine hyperoxidation rewires communication pathways in the nucleosome and destabilizes the dyad

Yasaman Karami , Emmanuelle Bignon

Computational and Structural Biotechnology Journal, 2024, 23, pp.1387-1396. ⟨10.1016/j.csbj.2024.03.025⟩

Article dans une revue hal-04567034v1
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The hinge-engineered IgG1-IgG3 hybrid subclass IgGh47 potently enhances Fc-mediated function of anti-streptococcal and SARS-CoV-2 antibodies

Arman Izadi , Yasaman Karami , Eleni Bratanis , Sebastian Wrighton , Hamed Khakzad et al.

Nature Communications, 2024, 15 (1), pp.3600. ⟨10.1038/s41467-024-47928-8⟩

Article dans une revue hal-04567019v1
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Exploring a Structural Data Mining Approach to Design Linkers for Head-to-Tail Peptide Cyclization

Yasaman Karami , Samuel Murail , Julien Giribaldi , Benjamin Lefranc , Florian Defontaine et al.

Journal of Chemical Information and Modeling, 2023, 63 (20), pp.6436-6450. ⟨10.1021/acs.jcim.3c00865⟩

Article dans une revue (article de synthèse) hal-04406845v1
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Bat coronaviruses related to SARS-CoV-2 and infectious for human cells

Sarah Temmam , Khamsing Vongphayloth , Eduard Baquero , Sandie Munier , Massimiliano Bonomi et al.

Nature, 2022, 604 (7905), pp.330-336. ⟨10.1038/s41586-022-04532-4⟩

Article dans une revue pasteur-03661247v1
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Structural determination of Streptococcus pyogenes M1 protein interactions with human immunoglobulin G using integrative structural biology

Hamed Khakzad , Lotta Happonen , Yasaman Karami , Sounak Chowdhury , Gizem Ertürk Bergdahl et al.

PLoS Computational Biology, 2021, 17 (1), pp.e1008169. ⟨10.1371/journal.pcbi.1008169⟩

Article dans une revue hal-04429695v1
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Computational and biochemical analysis of type IV pilus dynamics and stability

Yasaman Karami , Aracelys López-Castilla , Andrea Ori , Jenny-Lee Thomassin , Benjamin Bardiaux et al.

Structure, 2021, 29, pp.1-13. ⟨10.1016/j.str.2021.07.008⟩

Article dans une revue pasteur-03380000v2
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Automatic Bayesian Weighting for SAXS Data

Yannick G Spill , Yasaman Karami , Pierre Maisonneuve , Nicolas Wolff , Michael Nilges

Frontiers in Molecular Biosciences, 2021, 8, pp.671011. ⟨10.3389/fmolb.2021.671011⟩

Article dans une revue hal-03268506v1
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Predicting substitutions to modulate disorder and stability in coiled-coils

Yasaman Karami , Paul Saighi , Rémy Vanderhaegen , Denis Gerlier , Sonia Longhi et al.

BMC Bioinformatics, 2020, 21 (S19), pp.573. ⟨10.1186/s12859-020-03867-x⟩

Article dans une revue hal-03154196v2
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DaReUS-Loop: a web server to model multiple loops in homology models

Yasaman Karami , Julien Rey , Guillaume Postic , Samuel Murail , Pierre Tuffery et al.

Nucleic Acids Research, 2019, 47 (W1), pp.423-428. ⟨10.1093/nar/gkz403⟩

Article dans une revue hal-03201549v1
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GEMME: A Simple and Fast Global Epistatic Model Predicting Mutational Effects

Elodie Laine , Yasaman Karami , Alessandra Carbone

Molecular Biology and Evolution, 2019, 36 (11), pp.2604-2619. ⟨10.1093/molbev/msz179⟩

Article dans une revue hal-02431792v1
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DaReUS-Loop: accurate loop modeling using fragments from remote or unrelated proteins

Yasaman Karami , Frédéric Guyon , Sjoerd de Vries , Pierre Tufféry

Scientific Reports, 2018, 8 (1), pp.13673. ⟨10.1038/s41598-018-32079-w⟩

Article dans une revue hal-03824438v1
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“Infostery” analysis of short molecular dynamics simulations identifies highly sensitive residues and predicts deleterious mutations

Yasaman Karami , Tristan Bitard-Feildel , Elodie Laine , Alessandra Carbone

Scientific Reports, 2018, 8 (1), pp.16126 (2018). ⟨10.1038/s41598-018-34508-2⟩

Article dans une revue hal-01911176v1
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Dissecting protein architecture with communication blocks and communicating segment pairs

Yasaman Karami , Elodie Laine , Alessandra Carbone

BMC Bioinformatics, 2016, 17 (S2), pp.133-148. ⟨10.1186/s12859-015-0855-y⟩

Article dans une revue hal-01260475v1

Structure and Dynamics of Type 4a Pili and Type 2 Secretion System Endopili

Nadia Izadi-Pruneyre , Yasaman Karami , Michael Nilges

Macromolecular Protein Complexes V, 104, Springer International Publishing, pp.549-563, 2024, Subcellular Biochemistry, 978-3-031-58842-6. ⟨10.1007/978-3-031-58843-3_21⟩

Chapitre d'ouvrage hal-04671491v1