Yasaman Karami

Publications

Article dans une revue (19)

DynamicGT: A dynamic-aware geometric transformer model to predict protein-binding interfaces in flexible and disordered regions Omid Mokhtari,Sergei Grudinin,Yasaman Karami,Hamed Khakzad Cell Systems, 2026, 17 (1), pp.101454. ⟨10.1016/j.cels.2025.101454⟩ Article dans une revue hal-05553086v1
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
B3GALT6 mutations lead to compromised connective tissue biomechanics in Ehlers-Danlos syndrome Roméo Milan Diana,Benjamin Jolivet,Jean-Baptiste Vincourt,Sébastien Hergalant,Grégory Franciuset al. JCI Insight, 2025, 10 (16), pp.e179474. ⟨10.1172/jci.insight.179474⟩ Article dans une revue hal-05234907v1
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 Vuillonet al. Biomolecules, 2025, 15 (4), pp.541. ⟨10.3390/biom15040541⟩ Article dans une revue hal-05041555v1
Stoichiometric insights into SARS-CoV-2 spike–ACE2 binding across variants Ishola Abeeb Akinwumi,Sneha Bheemireddy,Laurent Chaloin,Serge Pérez,Hamed Khakzadet al. Computational and Structural Biotechnology Journal, 2025, 27, pp.3285-3291. ⟨10.1016/j.csbj.2025.07.034⟩ Article dans une revue hal-05236496v1
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 Khakzadet al. Nature Communications, 2024, 15 (1), pp.3600. ⟨10.1038/s41467-024-47928-8⟩ Article dans une revue hal-04567019v1
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
Exploring a Structural Data Mining Approach to Design Linkers for Head-to-Tail Peptide Cyclization Yasaman Karami,Samuel Murail,Julien Giribaldi,Benjamin Lefranc,Florian Defontaineet 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
Bat coronaviruses related to SARS-CoV-2 and infectious for human cells Sarah Temmam,Khamsing Vongphayloth,Eduard Baquero,Sandie Munier,Massimiliano Bonomiet al. Nature, 2022, 604 (7905), pp.330-336. ⟨10.1038/s41586-022-04532-4⟩ Article dans une revue pasteur-03661247v1
Computational and biochemical analysis of type IV pilus dynamics and stability Yasaman Karami,Aracelys López-Castilla,Andrea Ori,Jenny-Lee Thomassin,Benjamin Bardiauxet al. Structure, 2021, 29, pp.1-13. ⟨10.1016/j.str.2021.07.008⟩ Article dans une revue pasteur-03380000v2
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 Bergdahlet al. PLoS Computational Biology, 2021, 17 (1), pp.e1008169. ⟨10.1371/journal.pcbi.1008169⟩ Article dans une revue hal-04429695v1
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
Predicting substitutions to modulate disorder and stability in coiled-coils Yasaman Karami,Paul Saighi,Rémy Vanderhaegen,Denis Gerlier,Sonia Longhiet al. BMC Bioinformatics, 2020, 21 (S19), pp.573. ⟨10.1186/s12859-020-03867-x⟩ Article dans une revue hal-03154196v2
DaReUS-Loop: a web server to model multiple loops in homology models Yasaman Karami,Julien Rey,Guillaume Postic,Samuel Murail,Pierre Tufferyet al. Nucleic Acids Research, 2019, 47 (W1), pp.423-428. ⟨10.1093/nar/gkz403⟩ Article dans une revue hal-03201549v1
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
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
“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
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

Chapitre d'ouvrage (1)

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

Pré-publication, Document de travail (4)

DynamicGT: a dynamic-aware geometric transformer model to predict protein binding interfaces in flexible and disordered regions Omid Mokhtari,Sergei Grudinin,Yasaman Karami,Hamed Khakzad 2025 Pré-publication, Document de travail hal-05041563v1
Cumulating MS Signal enables polyclonal antibody analysis Carlos Gueto-Tettay,Joel Ströbaek,Di Tang,Alejandro Gomez Toledo,Yasaman Karamiet al. 2025 Pré-publication, Document de travail hal-05041560v1
Histone H3 as a redox switch in the nucleosome core particle: insights from molecular modeling † Yasaman Karami,Roy González-Alemán,Mailys Duch,Yuya Qiu,Yani Kedjaret al. 2024 Pré-publication, Document de travail hal-04746825v1
Coronaviruses with a SARS-CoV-2-like receptor-binding domain allowing ACE2-mediated entry into human cells isolated from bats of Indochinese peninsula Sarah Temmam,Khamsing Vongphayloth,Eduard Baquero Salazar,Sandie Munier,Massimiliano Bonomiet al. 2021 Pré-publication, Document de travail hal-03417488v1