2024
Journal articles
- titre
- The hinge-engineered IgG1-IgG3 hybrid subclass IgGh47 potently enhances Fc-mediated function of anti-streptococcal and SARS-CoV-2 antibodies
- auteur
- Arman Izadi, Yasaman Karami, Eleni Bratanis, Sebastian Wrighton, Hamed Khakzad, Maria Nyblom, Berit Olofsson, Lotta Happonen, Di Tang, Martin Sundwall, Magdalena Godzwon, Yashuan Chao, Alejandro Gomez Toledo, Tobias Schmidt, Mats Ohlin, Michael Nilges, Johan Malmström, Wael Bahnan, Oonagh Shannon, Lars Malmström, Pontus Nordenfelt
- article
- Nature Communications, 2024, 15 (1), pp.3600. ⟨10.1038/s41467-024-47928-8⟩
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- Journal articles
- DOI
- DOI : 10.1038/s41467-024-47928-8
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2023
Journal articles
- titre
- A new age in protein design empowered by deep learning
- auteur
- Hamed Khakzad, Ilia Igashov, Arne Schneuing, Casper Goverde, Michael Bronstein, Bruno Correia
- article
- Cell Systems, 2023, 14 (11), pp.925-939. ⟨10.1016/j.cels.2023.10.006⟩
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- Journal articles
- DOI
- DOI : 10.1016/j.cels.2023.10.006
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- titre
- Shigella IpaA mediates actin bundling through diffusible vinculin oligomers with activation imprint
- auteur
- Cesar Valencia-Gallardo, Daniel-Isui Aguilar-Salvador, Hamed Khakzad, Benjamin Cocom-Chan, Charles Bou-Nader, Christophe Velours, Yosra Zarrouk, Christophe Le Clainche, Christian Malosse, Diogo Borges Lima, Nicole Quenech’du, Bilal Mazhar, Sami Essid, Marc Fontecave, Atef Asnacios, Julia Chamot-Rooke, Lars Malmström, Guy Tran van Nhieu
- article
- Cell Reports, 2023, 42 (4), pp.112405. ⟨10.1016/j.celrep.2023.112405⟩
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- Journal articles
- DOI
- DOI : 10.1016/j.celrep.2023.112405
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- titre
- Multienzyme deep learning models improve peptide de novo sequencing by mass spectrometry proteomics
- auteur
- Carlos Gueto-Tettay, Di Tang, Lotta Happonen, Moritz Heusel, Hamed Khakzad, Johan Malmström, Lars Malmström
- article
- PLoS Computational Biology, 2023, 19 (1), pp.e1010457. ⟨10.1371/journal.pcbi.1010457⟩
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- Journal articles
- DOI
- DOI : 10.1371/journal.pcbi.1010457
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2022
Journal articles
- titre
- Invasive Streptococcal Infection Can Lead to the Generation of Cross-Strain Opsonic Antibodies
- auteur
- Therese de Neergaard, Anna Bläckberg, Hanna Ivarsson, Sofia Thomasson, Vibha Kumra Ahnlide, Sounak Chowdhury, Hamed Khakzad, Wael Bahnan, Johan Malmström, Magnus Rasmussen, Pontus Nordenfelt
- article
- Microbiology Spectrum, 2022, 10 (6), ⟨10.1128/spectrum.02486-22⟩
- typdoc
- Journal articles
- DOI
- DOI : 10.1128/spectrum.02486-22
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- titre
- A human monoclonal antibody bivalently binding two different epitopes in streptococcal M protein mediates immune function
- auteur
- Wael Bahnan, Lotta Happonen, Hamed Khakzad, Vibha Kumra Ahnlide, Therese de Neergaard, Sebastian Wrighton, Oscar André, Eleni Bratanis, Di Tang, Thomas Hellmark, Lars Björck, Oonagh Shannon, Lars Malmström, Johan Malmström, Pontus Nordenfelt
- article
- EMBO Molecular Medicine, 2022, 15 (2), ⟨10.15252/emmm.202216208⟩
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- Journal articles
- DOI
- DOI : 10.15252/emmm.202216208
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- titre
- Spike-Dependent Opsonization Indicates Both Dose-Dependent Inhibition of Phagocytosis and That Non-Neutralizing Antibodies Can Confer Protection to SARS-CoV-2
- auteur
- Wael Bahnan, Sebastian Wrighton, Martin Sundwall, Anna Bläckberg, Olivia Larsson, Urban Höglund, Hamed Khakzad, Magdalena Godzwon, Maria Walle, Elisabeth Elder, Anna Söderlund Strand, Lotta Happonen, Oscar André, Johannes Kumra Ahnlide, Thomas Hellmark, Vidar Wendel-Hansen, Robert Pa. Wallin, Johan Malmstöm, Lars Malmström, Mats Ohlin, Magnus Rasmussen, Pontus Nordenfelt
- article
- Frontiers in Immunology, 2022, 12, ⟨10.3389/fimmu.2021.808932⟩
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- Journal articles
- DOI
- DOI : 10.3389/fimmu.2021.808932
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2021
Journal articles
- titre
- Cheetah-MS: a web server to model protein complexes using tandem cross-linking mass spectrometry data
- auteur
- Hamed Khakzad, Lotta Happonen, Johan Malmström, Lars Malmström
- article
- Bioinformatics, 2021, 37 (24), pp.4871-4872. ⟨10.1093/bioinformatics/btab449⟩
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- Journal articles
- DOI
- DOI : 10.1093/bioinformatics/btab449
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- titre
- Streptococcus pyogenes Forms Serotype- and Local Environment-Dependent Interspecies Protein Complexes
- auteur
- Sounak Chowdhury, Hamed Khakzad, Gizem Ertürk Bergdahl, Rolf Lood, Simon Ekstrom, Dirk Linke, Lars Malmström, Lotta Happonen, Johan Malmström
- article
- mSystems, 2021, 6 (5), ⟨10.1128/msystems.00271-21⟩
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- Journal articles
- DOI
- DOI : 10.1128/msystems.00271-21
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- titre
- Quaternary Structure Modeling Through Chemical Cross-Linking Mass Spectrometry: Extending TX-MS Jupyter Reports
- auteur
- Hamed Khakzad, Swen Vermeul, Lars Malmström
- article
- Journal of visualized experiments : JoVE, 2021, 176, ⟨10.3791/60311⟩
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- Journal articles
- DOI
- DOI : 10.3791/60311
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- titre
- In vivo Cross-Linking MS of the Complement System MAC Assembled on Live Gram-Positive Bacteria
- auteur
- Hamed Khakzad, Lotta Happonen, Guy Tran van Nhieu, Johan Malmström, Lars Malmström
- article
- Frontiers in Genetics, 2021, 11, ⟨10.3389/fgene.2020.612475⟩
- typdoc
- Journal articles
- DOI
- DOI : 10.3389/fgene.2020.612475
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- titre
- Structural determination of Streptococcus pyogenes M1 protein interactions with human immunoglobulin G using integrative structural biology
- auteur
- Hamed Khakzad, Lotta Happonen, Yasaman Karami, Sounak Chowdhury, Gizem Ertürk Bergdahl, Michael Nilges, Guy Tran van Nhieu, Johan Malmström, Lars Malmström
- article
- PLoS Computational Biology, 2021, 17 (1), pp.e1008169. ⟨10.1371/journal.pcbi.1008169⟩
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- Journal articles
- DOI
- DOI : 10.1371/journal.pcbi.1008169
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- titre
- The structure of human dermatan sulfate epimerase 1 emphasizes the importance of C5-epimerization of glucuronic acid in higher organisms
- auteur
- Mahmudul Hasan, Hamed Khakzad, Lotta Happonen, Anders Sundin, Johan Unge, Uwe Mueller, Johan Malmström, Gunilla Westergren-Thorsson, Lars Malmström, Ulf Ellervik, Anders Malmström, Emil Tykesson
- article
- Chemical Science, 2021, 12 (5), pp.1869-1885. ⟨10.1039/D0SC05971D⟩
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- Journal articles
- DOI
- DOI : 10.1039/D0SC05971D
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Preprints, Working Papers, …
- titre
- ipaA triggers vinculin oligomerization to strengthen cell adhesion during Shigella invasion
- auteur
- Cesar Valencia-Gallardo, Daniel-Isui Aguilar-Salvador, Hamed Khakzad, Charles Bou-Nader, Christian Malosse, Diogo Borges Lima, Chakir Bello, Benjamin Cocom-Chan, Nicole Quenech’du, Bilal Mazhar, Delphine Javelaud, Jacques Fattaccioli, Alain Mauviel, Marc Fontecave, Atef Asnacios, Julia Chamot-Rooke, Lars Malmström, Guy Tran van Nhieu
- article
- 2021
- typdoc
- Preprints, Working Papers, …
- DOI
- DOI : 10.1101/773283
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2020
Journal articles
- titre
- Macromolecular modeling and design in Rosetta: recent methods and frameworks
- auteur
- Julia Koehler Leman, Brian Weitzner, Steven Lewis, Jared Adolf-Bryfogle, Nawsad Alam, Rebecca Alford, Melanie Aprahamian, David Baker, Kyle Barlow, Patrick Barth, Benjamin Basanta, Brian Bender, Kristin Blacklock, Jaume Bonet, Scott Boyken, Phil Bradley, Chris Bystroff, Patrick Conway, Seth Cooper, Bruno Correia, Brian Coventry, Rhiju Das, René de Jong, Frank Dimaio, Lorna Dsilva, Roland Dunbrack, Alexander Ford, Brandon Frenz, Darwin Fu, Caleb Geniesse, Lukasz Goldschmidt, Ragul Gowthaman, Jeffrey Gray, Dominik Gront, Sharon Guffy, Scott Horowitz, Po-Ssu Huang, Thomas Huber, Tim Jacobs, Jeliazko Jeliazkov, David Johnson, Kalli Kappel, John Karanicolas, Hamed Khakzad, Karen Khar, Sagar Khare, Firas Khatib, Alisa Khramushin, Indigo King, Robert Kleffner, Brian Koepnick, Tanja Kortemme, Georg Kuenze, Brian Kuhlman, Daisuke Kuroda, Jason Labonte, Jason Lai, Gideon Lapidoth, Andrew Leaver-Fay, Steffen Lindert, Thomas Linsky, Nir London, Joseph Lubin, Sergey Lyskov, Jack Maguire, Lars Malmström, Enrique Marcos, Orly Marcu, Nicholas Marze, Jens Meiler, Rocco Moretti, Vikram Khipple Mulligan, Santrupti Nerli, Christoffer Norn, Shane Ó’conchúir, Noah Ollikainen, Sergey Ovchinnikov, Michael Pacella, Xingjie Pan, Hahnbeom Park, Ryan Pavlovicz, Manasi Pethe, Brian Pierce, Kala Bharath Pilla, Barak Raveh, P. Douglas Renfrew, Shourya Burman, Aliza Rubenstein, Marion Sauer, Andreas Scheck, William Schief, Ora Schueler-Furman, Yuval Sedan, Alexander Sevy, Nikolaos Sgourakis, Lei Shi, Justin Siegel, Daniel-Adriano Silva, Shannon Smith, Yifan Song, Amelie Stein, Maria Szegedy, Frank Teets, Summer Thyme, Ray Yu-Ruei Wang, Andrew Watkins, Lior Zimmerman, Richard Bonneau
- article
- Nature Methods, 2020, 17 (7), pp.665-680. ⟨10.1038/s41592-020-0848-2⟩
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- DOI
- DOI : 10.1038/s41592-020-0848-2
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- titre
- Structural proteomics, electron cryo-microscopy and structural modeling approaches in bacteria–human protein interactions
- auteur
- Sounak Chowdhury, Lotta Happonen, Hamed Khakzad, Lars Malmström, Johan Malmström
- article
- Medical Microbiology and Immunology, 2020, 209 (3), pp.265-275. ⟨10.1007/s00430-020-00663-5⟩
- typdoc
- Journal articles
- DOI
- DOI : 10.1007/s00430-020-00663-5
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2019
Journal articles
- titre
- A quantitative Streptococcus pyogenes–human protein–protein interaction map reveals localization of opsonizing antibodies
- auteur
- Lotta Happonen, Simon Hauri, Gabriel Svensson Birkedal, Christofer Karlsson, Therese de Neergaard, Hamed Khakzad, Pontus Nordenfelt, Mats Wikström, Magdalena Wisniewska, Lars Björck, Lars Malmström, Johan Malmström
- article
- Nature Communications, 2019, 10 (1), pp.2727. ⟨10.1038/s41467-019-10583-5⟩
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- Journal articles
- DOI
- DOI : 10.1038/s41467-019-10583-5
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- titre
- Greedy de novo motif discovery to construct motif repositories for bacterial proteomes
- auteur
- Hamed Khakzad, Johan Malmström, Lars Malmström
- article
- BMC Bioinformatics, 2019, 20 (S4), pp.141. ⟨10.1186/s12859-019-2686-8⟩
- typdoc
- Journal articles
- DOI
- DOI : 10.1186/s12859-019-2686-8
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- titre
- Rapid determination of quaternary protein structures in complex biological samples
- auteur
- Simon Hauri, Hamed Khakzad, Lotta Happonen, Johan Teleman, Johan Malmström, Lars Malmström
- article
- Nature Communications, 2019, 10 (1), pp.192. ⟨10.1038/s41467-018-07986-1⟩
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- Journal articles
- DOI
- DOI : 10.1038/s41467-018-07986-1
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2016
Journal articles
- titre
- PDB2Graph: A toolbox for identifying critical amino acids map in proteins based on graph theory
- auteur
- Niloofar Niknam, Hamed Khakzad, Seyed Shahriar Arab, Hossein Naderi-Manesh
- article
- Computers in Biology and Medicine, 2016, 72, pp.151-159. ⟨10.1016/j.compbiomed.2016.03.012⟩
- typdoc
- Journal articles
- DOI
- DOI : 10.1016/j.compbiomed.2016.03.012
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