Andrelab

Publications

  • 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. 

Andrelab

We combine computational and experimental methods to understand the structure, interactions and evolution of proteins.
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