Amelie Stein

Amelie Stein

Associate Professor

ORCID: 0000-0002-5862-1681

Publication year:
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1 - 37 out of 37Page size: 500
  1. 2024
  2. Published

    A mutational atlas for Parkin proteostasis

    Clausen, L., Voutsinos, Vasileios, Cagiada, Matteo, Johansson, Kristoffer Enøe, Grønbæk-Thygesen, Martin, Nariya, S., Powell, R. L., Have, M. K. N., Østergaard, Vibe Hallundbæk, Stein, Amelie, Fowler, D. M., Lindorff-Larsen, Kresten & Hartmann-Petersen, Rasmus, 2024, In: Nature Communications. 15, 1, 17 p., 1541.

    Research output: Contribution to journal › Journal article › Research › peer-review

  3. 2023
  4. Published

    A comprehensive map of human glucokinase variant activity

    Andersen, Sarah Gersing, Cagiada, Matteo, Gebbia, M., Gjesing, A. P., Coté, A. G., Seesankar, G., Li, R., Tabet, D., Weile, J., Stein, Amelie, Gloyn, A. L., Hansen, Torben, Roth, F. P., Lindorff-Larsen, Kresten & Hartmann-Petersen, Rasmus, 2023, In: Genome Biology. 24, 1, 23 p., 97.

    Research output: Contribution to journal › Journal article › Research › peer-review

  5. Published

    Accurate protein stability predictions from homology models

    Valanciute, A., Nygaard, L., Zschach, Henrike, Maglegaard Jepsen, M., Lindorff-Larsen, Kresten & Stein, Amelie, 2023, In: Computational and Structural Biotechnology Journal. 21, p. 66-73 8 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  6. Published

    Discovering functionally important sites in proteins

    Cagiada, Matteo, Bottaro, S., Lindemose, Søren, Schenstrøm, S. M., Stein, Amelie, Hartmann-Petersen, Rasmus & Lindorff-Larsen, Kresten, 2023, In: Nature Communications. 14, 1, 13 p., 4175.

    Research output: Contribution to journal › Journal article › Research › peer-review

  7. Published

    HSP70-binding motifs function as protein quality control degrons

    Abildgaard, A. B., Voutsinos, Vasileios, Petersen, S. D., Larsen, Fia Brunsgaard Valsted, Kampmeyer, Caroline, Johansson, Kristoffer Enøe, Stein, Amelie, Ravid, T., Andréasson, C., Jensen, M. K., Lindorff-Larsen, Kresten & Hartmann-Petersen, Rasmus, 2023, In: Cellular and Molecular Life Sciences. 80, 1, 17 p., 32.

    Research output: Contribution to journal › Journal article › Research › peer-review

  8. Published

    Interpreting the molecular mechanisms of disease variants in human transmembrane proteins

    Tiemann, Johanna Katarina Sofie, Zschach, Henrike, Lindorff-Larsen, Kresten & Stein, Amelie, 2023, In: Biophysical Journal. 122, 11, 16 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  9. Published

    Lynch syndrome, molecular mechanisms and variant classification

    Abildgaard, A. B., Nielsen, S., Bernstein, I., Stein, Amelie, Lindorff-Larsen, Kresten & Hartmann-Petersen, Rasmus, 2023, In: British Journal of Cancer. 128, 9 p.

    Research output: Contribution to journal › Review › Research › peer-review

  10. Published

    Mind the gap

    Larsen-Ledet, Sven & Stein, Amelie, 2023, In: Structure. 31, 6, p. 641-643 3 p.

    Research output: Contribution to journal › Comment/debate › Research › peer-review

  11. Published

    Rapid protein stability prediction using deep learning representations

    Blaabjerg, Lasse Møller, Kassem, M. M., Good, L. L., Jonsson, Nicolas, Cagiada, Matteo, Johansson, Kristoffer Enøe, Boomsma, Wouter, Stein, Amelie & Lindorff-Larsen, Kresten, 2023, In: eLife. 12, 19 p., e82593.

    Research output: Contribution to journal › Journal article › Research › peer-review

  12. Published

    Rare Catechol-O-methyltransferase Missense Variants Are Structurally Unstable Proteasome Targets

    Larsen, Fia Brunsgaard Valsted, Cagiada, Matteo, Dideriksen, J., Stein, Amelie, Lindorff-Larsen, Kresten & Hartmann-Petersen, Rasmus, 2023, In: Biochemistry. 62, 8, 12 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  13. 2022
  14. Published

    A structural biology community assessment of AlphaFold2 applications

    Akdel, M., Pires, D. E., Porta Pardo, E., Jänes, J., Zalevsky, A. O., Meszaros, B., Bryant, P., Good, L. L., Laskowski, R. A., Pozzati, G., Shenoy, A., Zhu, W., Kundrotas, P., Serra, V. R., Rodrigues, C. H. M., Dunham, A. S., Burke, D., Borkakoti, N., Velankar, S., Frost, A. & 14 others, Basquin, J., Lindorff-Larsen, Kresten, Bateman, A., Kajava, A., Valencia, A., Ovchinnikov, S., Durairaj, J., Ascher, D. B., Thornton, J. M., Davey, N. E., Stein, Amelie, Elofsson, A., Croll, T. & Beltrao, P., 2022, In: Nature Structural & Molecular Biology. 29, 11, 16 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  15. Published

    Co-evolution of drug resistance and broadened substrate recognition in HIV protease variants isolated from an Escherichia coli genetic selection system

    Koivisto, J. M., Poulsen, N. R., Larsen, B. S., Weibull, M. G. M., Stein, Amelie, Doro, F., Winther, Jakob R., Lindorff-Larsen, Kresten & Willemoës, Martin, 2022, In: The Biochemical journal. 479, 4, p. 479-501

    Research output: Contribution to journal › Journal article › Research › peer-review

  16. Published

    Disease-linked mutations cause exposure of a protein quality control degron

    Kampmeyer, Caroline, Larsen-Ledet, Sven, Wagnkilde, M. R., Michelsen, M., Iversen, Henriette Kring Mangor, Nielsen, S. V., Lindemose, Søren, Caregnato, A., Ravid, T., Stein, Amelie, Teilum, Kaare, Lindorff-Larsen, Kresten & Hartmann-Petersen, Rasmus, 2022, In: Structure. 30, 9, p. 1245-1253.e5

    Research output: Contribution to journal › Journal article › Research › peer-review

  17. Published

    Predicting and interpreting large-scale mutagenesis data using analyses of protein stability and conservation

    Høie, M. H., Cagiada, Matteo, Frederiksen, A. H. B., Stein, Amelie & Lindorff-Larsen, Kresten, 2022, In: Cell Reports. 38, 2, 15 p., 110207.

    Research output: Contribution to journal › Journal article › Research › peer-review

  18. 2021
  19. Published

    Disorder in a two-domain neuronal Ca2+-binding protein regulates domain stability and dynamics using ligand mimicry

    Staby, L., Kemplen, K. R., Stein, Amelie, Ploug, Michael, Clarke, J., Skriver, Karen, Heidarsson, P. O. & Kragelund, Birthe Brandt, 2021, In: Cellular and molecular life sciences : CMLS. 78, p. 2263-2278 16 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  20. Published

    Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks

    Koehler Leman, J., Lyskov, S., Lewis, S. M., Adolf-Bryfogle, J., Alford, R. F., Barlow, K., Ben-Aharon, Z., Farrell, D., Fell, J., Hansen, W. A., Harmalkar, A., Jeliazkov, J., Kuenze, G., Krys, J. D., Ljubetič, A., Loshbaugh, A. L., Maguire, J., Moretti, R., Mulligan, V. K., Nance, M. L. & 30 others, Nguyen, P. T., Ó Conchúir, S., Roy Burman, S. S., Samanta, R., Smith, S. T., Teets, F., Tiemann, Johanna Katarina Sofie, Watkins, A., Woods, H., Yachnin, B. J., Bahl, C. D., Bailey-Kellogg, C., Baker, D., Das, R., DiMaio, F., Khare, S. D., Kortemme, T., Labonte, J. W., Lindorff-Larsen, Kresten, Meiler, J., Schief, W., Schueler-Furman, O., Siegel, J. B., Stein, Amelie, Yarov-Yarovoy, V., Kuhlman, B., Leaver-Fay, A., Gront, D., Gray, J. J. & Bonneau, R., 2021, In: Nature Communications. 12, 15 p., 6947.

    Research output: Contribution to journal › Journal article › Research › peer-review

  21. Published

    Mapping the degradation pathway of a disease-linked aspartoacylase variant

    Andersen, Sarah Gersing, Wang, Yong, Grønbæk-Thygesen, Martin, Kampmeyer, Caroline, Bjørnkjær, Lene, Willemoës, Martin, Andréasson, C., Stein, Amelie, Lindorff-Larsen, Kresten & Hartmann-Petersen, Rasmus, 2021, In: PLOS Genetics. 17, 4, 28 p., e1009539.

    Research output: Contribution to journal › Journal article › Research › peer-review

  22. Published

    Multiplexed assays reveal effects of missense variants in MSH2 and cancer predisposition

    Nielsen, S. V., Hartmann-Petersen, Rasmus, Stein, Amelie & Lindorff-Larsen, Kresten, 2021, In: PLOS Genetics. 17, 4, 6 p., e1009496.

    Research output: Contribution to journal › Journal article › Research › peer-review

  23. Published

    Understanding the Origins of Loss of Protein Function by Analyzing the Effects of Thousands of Variants on Activity and Abundance

    Cagiada, Matteo, Johansson, Kristoffer Enøe, Valanciute, A., Nielsen, S. V., Hartmann-Petersen, Rasmus, Yang, J. J., Fowler, D. M., Stein, Amelie & Lindorff-Larsen, Kresten, 2021, In: Molecular Biology and Evolution. 38, 8, p. 3235-3246

    Research output: Contribution to journal › Journal article › Research › peer-review

  24. 2020
  25. Published

    24 Messages on a Sustainable Career in Research at UCPH

    Larsen, K. R. (ed.), Wegener, H. C., Stein, A., Bach, A., Williams, A. R., Gall, C., Gravert, C., Gloriam, D. E., Lorenzen, E., Yvanez, E., Cappellini, E., Poulsen, F., Mortensen, J., Bentzen, J. S., Shik, J. Z., Miskowiak, K. W., Elgaard, K. K. E., Jønsson, K. A., Won, K. J., Nørgaard, L. C. & 9 others, Cantarero Arevalo, Lourdes, Kristiansen, Maria, Lund, Marianne N., Borregaard, Michael Krabbe, Høyland-Kroghsbo, Nina Molin, Iversen, Rune, Viskum, U., Nosch, Marie Louise Bech & Hjorth, Jens, 2020, University of Copenhagen. 31 p.

    Research output: Book/Report › Report › Communication

  26. Published

    Classifying disease-associated variants using measures of protein activity and stability

    Jepsen, M. M., Fowler, D. M., Hartmann-Petersen, Rasmus, Stein, Amelie & Lindorff-Larsen, Kresten, 2020, Protein Homeostasis Diseases: Mechanisms and Novel Therapies. Pey, A. L. (ed.). Elsevier, p. 91-107

    Research output: Chapter in Book/Report/Conference proceeding › Book chapter › Research › peer-review

  27. Published

    Co-Chaperones in Targeting and Delivery of Misfolded Proteins to the 26S Proteasome

    Abildgaard, A. B., Andersen, Sarah Gersing, Larsen-Ledet, Sven, Nielsen, S. V., Stein, Amelie, Lindorff-Larsen, Kresten & Hartmann-Petersen, Rasmus, 2020, In: Biomolecules. 10, 8, 24 p., 1141.

    Research output: Contribution to journal › Review › Research › peer-review

  28. Published

    Folliculin variants linked to Birt-Hogg-Dubé syndrome are targeted for proteasomal degradation

    Bjørnkjær, Lene, Stein, Amelie, Grønbæk-Thygesen, Martin, Nygaard, L., Søltoft, C. L., Nielsen, S. V., Lisby, Michael, Ravid, T., Lindorff-Larsen, Kresten & Hartmann-Petersen, Rasmus, 2020, In: PLOS Genetics. 16, 11, 28 p., e1009187.

    Research output: Contribution to journal › Journal article › Research › peer-review

  29. Published

    Novel HARS2 missense variants identified in individuals with sensorineural hearing impairment and Perrault syndrome

    Karstensen, H. G., Rendtorff, N. D., Hindbæk, L. S., Colombo, R., Stein, Amelie, Birkebæk, N. H., Hartmann-Petersen, Rasmus, Lindorff-Larsen, Kresten, Højland, A. T., Petersen, M. B. & Tranebjærg, Lisbeth, 2020, In: European Journal of Medical Genetics. 63, 3, 6 p., 103733.

    Research output: Contribution to journal › Journal article › Research › peer-review

  30. Published

    Protein destabilization and degradation as a mechanism for hereditary disease

    Nielsen, S. V., Schenstrøm, S. M., Christensen, Caspar Elo, Stein, Amelie, Lindorff-Larsen, Kresten & Hartmann-Petersen, Rasmus, 2020, Protein Homeostasis Diseases: Mechanisms and Novel Therapies. Pey, A. L. (ed.). Elsevier, p. 111-125

    Research output: Chapter in Book/Report/Conference proceeding › Book chapter › Research › peer-review

  31. 2019
  32. Published

    Biophysical and Mechanistic Models for Disease-Causing Protein Variants

    Stein, Amelie, Fowler, D. M., Hartmann-Petersen, Rasmus & Lindorff-Larsen, Kresten, 2019, In: Trends in Biochemical Sciences. 44, 7, p. 575-588

    Research output: Contribution to journal › Review › Research › peer-review

  33. Published

    Computational and cellular studies reveal structural destabilization and degradation of MLH1 variants in Lynch syndrome

    Abildgaard, A. B., Stein, Amelie, Nielsen, S. V., Schultz-Knudsen, Katrine, Papaleo, E., Shrikhande, A., Hoffmann, Eva, Bernstein, I., Gerdes, Anne-Marie Axø, Takahashi, M., Ishioka, C., Lindorff-Larsen, Kresten & Hartmann-Petersen, Rasmus, 2019, In: eLife. 8, 28 p., e49138 .

    Research output: Contribution to journal › Journal article › Research › peer-review

  34. Published

    Protein stability and degradation in health and disease

    Bjørnkjær, Lene, Abildgaard, A. B., Gersing, S. K., Stein, Amelie, Lindorff-Larsen, Kresten & Hartmann-Petersen, Rasmus, 2019, Molecular Chaperones in Human Disorders. Donev, R. (ed.). Academic Press, p. 61-83 (Advances in Protein Chemistry and Structural Biology, Vol. 114).

    Research output: Chapter in Book/Report/Conference proceeding › Book chapter › Research › peer-review

  35. Published

    Toward mechanistic models for genotype-phenotype correlations in phenylketonuria using protein stability calculations

    Scheller, R., Stein, Amelie, Nielsen, S. V., Marin, F. I., Gerdes, Anne-Marie Axø, Di Marco, M., Papaleo, E., Lindorff-Larsen, Kresten & Hartmann-Petersen, Rasmus, 2019, In: Human Mutation. 40, 4, p. 444-457

    Research output: Contribution to journal › Journal article › Research › peer-review

  36. 2018
  37. Published

    Random mutagenesis analysis of the Influenza A M2 proton channel reveals novel resistance mutants

    Santner, P., Martins, J. M. D. S., Kampmeyer, Caroline, Hartmann-Petersen, Rasmus, Laursen, J. S., Stein, Amelie, Olsen, Christian Adam, Arkin, I. T., Winther, Jakob R., Willemoës, Martin & Lindorff-Larsen, Kresten, 2018, In: Biochemistry. 57, 41, p. 5957-5968

    Research output: Contribution to journal › Journal article › Research › peer-review

  38. 2017
  39. Published

    Blocking protein quality control to counter hereditary cancers

    Kampmeyer, Caroline, Nielsen, S. V., Bjørnkjær, Lene, Stein, Amelie, Gerdes, Anne-Marie Axø, Lindorff-Larsen, Kresten & Hartmann-Petersen, Rasmus, Dec 2017, In: Genes, Chromosomes & Cancer. 56, 12, p. 823-831 9 p.

    Research output: Contribution to journal › Review › Research › peer-review

  40. Published

    Predicting the impact of Lynch syndrome-causing missense mutations from structural calculations

    Nielsen, S. V., Stein, Amelie, Dinitzen, A. B., Papaleo, E., Tatham, M. H., Poulsen, E. G., Kassem, M. M., Rasmussen, Lene Juel, Lindorff-Larsen, Kresten & Hartmann-Petersen, Rasmus, 19 Apr 2017, In: PLoS Genetics. 13, 4, 26 p., e1006739.

    Research output: Contribution to journal › Journal article › Research › peer-review

  41. 2015

  42. Combined covalent-electrostatic model of hydrogen bonding improves structure prediction with Rosetta

    O'Meara, M. J., Leaver-Fay, A., Tyka, M. D., Stein, Amelie, Houlihan, K., DiMaio, F., Bradley, P., Kortemme, T., Baker, D., Snoeyink, J. & Kuhlman, B., 2015, In: Journal of Chemical Theory and Computation. 11, 2, p. 609-622 14 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  43. 2014

  44. 3did: a catalog of domain-based interactions of known three-dimensional structure

    Mosca, R., Céol, A., Stein, Amelie, Olivella, R. & Aloy, P., 2014, In: Nucleic Acids Research. 42, D1, p. D374-D379

    Research output: Contribution to journal › Journal article › Research › peer-review

  45. 2013

  46. Improvements to robotics-inspired conformational sampling in Rosetta

    Stein, Amelie & Kortemme, T., 2013, In: PLoS ONE. 8, 5, p. 1-13 e63090.

    Research output: Contribution to journal › Journal article › Research › peer-review

  47. 2010

  48. Novel peptide-mediated interactions derived from high-resolution 3-dimensional structures

    Stein, Amelie & Aloy, P., 20 May 2010, In: PLOS Computational Biology. 6, 5, p. e1000789

    Research output: Contribution to journal › Journal article › Research › peer-review

  49. Uncovering new substrates for Aurora A kinase

    Sardon, T., Pache, R. A., Stein, Amelie, Molina, H., Vernos, I. & Aloy, P., 2010, In: EMBO Reports. 11, 12, p. 977-984 8 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

ID: 144764550