Jeppesen M and André I. Accurate prediction of protein assembly structure by combining AlphaFold and symmetrical docking. Nature Commun. 2023 Dec 13;14(1):8283. [LINK]
S Christensen, C Wernersson, I André. Facile Method for High-throughput Identification of Stabilizing Mutations. Journal of Molecular Biology 435 (18), 168209. [LINK]
Peng Huang, Hannah Åbacka, Daniel Varela, Raminta Venskutonytė, Lotta Happonen, Jonathan S. Bogan, Pontus Gourdon, Mahmood R. Amiry-Moghaddam, Ingemar André, Karin Lindkvist-Petersson. The intracellular helical bundle of human glucose transporter GLUT4 is important for complex formation with ASPL. FEBS Open Bio. 2023 Nov;13(11):2094-2107.
Christoffer Norn and Ingemar André Atomistic simulation of protein evolution reveals sequence covariation and time-dependent fluctuations of site-specific substitution rates. PloS Computational Biology (2023).
Daniel Varela, Vera Karlin and Ingemar André. A memetic algorithm enables efficient local and global all-atom protein-protein docking with backbone and side-chain flexibility. Structure. 2022 Nov 3;30(11):1550-1558.e3. [LINK]
Signe Christensen, Sebastian Rämisch and Ingemar André. DnaK response to expression of protein mutants is dependent on translation rate and stability. Communications Biology (2022). [LINK]
Lattanzi V, André I, Gasser U, Dubackic M, Olsson U and Linse S. Amyloid β 42 fibril structure based on small angle scattering. Proceedings of the National Academy of Sciences of the United States of America. 2021 Nov 30;118(48) [LINK].
Møller MS, Vaag Olesen S, André I. An ultra-high affinity protein-protein interface displaying sequence-robustness. Protein Sci. 2021 Jun;30(6):1144-1156. [LINK]
Christoffer Norn, Ingemar André Douglas L. Theobald. A thermodynamic model of protein structure evolution explains empirical amino acid substitution matrices. Protein Science. 2021 Jul 4. [LINK]
Filip Ljung and Ingemar André. ZEAL: Protein structure alignment based on shape similarity. Bioinformatics. 2021 Mar 27. [LINK]
Diego A Leonardo, Italo A Cavini, Fernanda A Sala, Deborah C Mendonça, Higor V D Rosa, Patricia S Kumagai , Edson Crusca Jr, Napoleão F Valadares, Ivo A Marques, José Brandão-Neto, Claudia E Munte, Hans R Kalbitzer, Nicolas Soler, Isabel Usón, Ingemar André, Ana P U Araujo, Humberto D'Muniz Pereira, Richard C Garratt. Orientational Ambiguity in Septin Coiled Coils and its Structural Basis. J Mol Biol. 2021 Apr 30;433(9):166889. [LINK]
Annika Rogstam, Maria Nyblom, Signe Christensen, Celeste Sele, Vladimir O Talibov, Therese Lindvall, Anna Andersson Rasmussen, Ingemar André, Zoë Fisher, Wolfgang Knecht, Frank Kozielski. Crystal Structure of Non-Structural Protein 10 from Severe Acute Respiratory Syndrome Coronavirus-2. Int J Mol Sci. 2020 Oct 6;21(19):E7375. [LINK]
Ryan C Oliver, ,Wojciech Potrzebowski, Seyed Morteza Najibi, Martin Nors Pedersen, Lise Arleth, Najet Mahmoudi and Ingemar André. Assembly of Capsids from Hepatitis B Virus Core Protein Progresses through Highly Populated Intermediates in the Presence and Absence of RNA. ACS Nano 2020 Aug 25;14(8):10226-10238.[LINK]
Mehmeti M, Bergenfelz C, Källberg E, Millrud C, Björk P, Ivars F, Johansson-Lindbom B, Kjellström S, André I, Leandersson K. Wnt5a is a TLR2/4-ligand that induces tolerance in human myeloid cells. Commun Biol. 2019 May 9;2:176.
Lizatović R, Assent M, Barendregt A, Dahlin J, Bille A, Satzinger K, Tupina D, Heck AJR, Wennmalm S, André I. A Protein-Based Encapsulation System with Calcium-Controlled Cargo Loading and Detachment. Angew Chem Int Ed Engl. 2018 Aug 27;57(35):11334-11338. [LINK]
Potrzebowski W, Trewhella J, André I. Bayesian inference of protein conformational ensembles from limited structural data. PLoS Computational Biology. 2018. 14, 12, e1006641.
André I, Belic S. Computational assessment of folding energy landscapes in heterodimeric coiled coils. Proteins. 2018. July 86(7):790-801.
André I. Modeling the Structure of Helical Assemblies with Experimental Constraints in Rosetta. Methods Mol Biol. 2018;1764:475-489.
Regenthal P, Hansen JS, André I, Lindkvist-Petersson K. Thermal stability and structural changes in bacterial toxins responsible for food poisoning. PLoS One. 2017 Feb 16;12(2):e0172445.
Boelt SG, Norn C, Rasmussen MI, André I, Čiplys E, Slibinskas R, Houen G, Højrup P. Mapping the Ca(2+) induced structural change in calreticulin. J Proteomics. 2016 Jun 16;142:138-48.
Lizatović R, Aurelius O, Stenstrom O, Drakenberg T, Akke M, Logan DT and André I. A De Novo Designed Coiled-Coil Peptide with a Reversible pH-Induced Oligomerization Switch. Structure 2016; doi: 10.1016/j.str.2016.03.027.
Norn CN and André I. Computational design of protein self-assembly. Current Opinion in Structural Biology 2016; pp 39-45. doi:10.1016/j.sbi.2016.04.002.
Potrzebowski W, André I. "Automated determination of fibrillar structures by simultaneous model building and fiber diffraction refinement". Nat Methods. 2015; doi: 10.1038/nmeth.3399
Rämisch S, Lizatović R, André I. Automated de novo phasing and model building of coiled-coil proteins. Acta Cryst D. 2015;D71.
Kaltofen S, Li C, Huang PS, Serpell LC, Barth A, André I. Computational de novo design of a self-assembling Peptide with predefined structure. Journal of molecular biology. 2015;427:550-62.
Rämisch S, Weiniger U, Martinsson J, Akke M and Andre I "Computational design of Leucine-Rich Repeat proteins with a defined geometry" Proc Natl Acad Sci, 2014, pii: 201413638.
Rämisch S, Lizatovic and Andre I. "Exploring alternate states and oligomerization preferences of coiled-coils by de novo structure modeling" Proteins, 2014. doi: 10.1002/prot.24729
André I, Corn J. "The RosettaCon 2012 Special Collection: Code Writ on Water, Documentation Writ in Stone." PLoS One. 2013 Sep 26;8(9):e73775. doi: 10.1371/journal.pone.0073775.
King NP, Sheffler W, Sawaya MR, Vollmar BS, Sumida JP, André I, Gonen T, Yeates TO, Baker D. "Computational design of self-assembling protein nanomaterials with atomic level accuracy". (2012) Science. Jun 1;336(6085):1171-4.
Meisner J, Maehigashi T, Andre I, Dunham CM and Moran, Jr CP. “Structure of the Basal Components of a Novel Bacterial Transporter”. (2012) Proc Natl Acad Sci U S A. Apr 3;109(14):5446-51.
Elkin M, Andre I and Lukatsky, D. Energy Fluctuations Shape Free Energy of Nonspecific Biomolecular Interactions. Journal of Statistical Physics (2012), 10.1007/s10955-012-0421-1.
Dimaio F, Leaver-Fay A, Bradley P, Baker D, André I. Modeling Symmetric Macromolecular Structures in Rosetta3. PLoS One. 2011;6(6):e20450.