Julia Koehler Leman, PhD: Publications

29. Koehler Leman, J., Szczerbiak, P., Renfrew, P. D., Gligorijevic, V., Berenberg, D., Vatanen, T., Taylor, B. C., Chandler, C., Janssen, S., Pataki, A., Carriero, N., Fisk, I., Xavier, R. J., Knight, R., Bonneau, R. & Kosciolek, T. Sequence-structure-function relationships in the microbial protein universe. bioRxiv 2022.03.18.484903 (2022). doi:10.1101/2022.03.18.484903. Under review – 550 views on 1st day on bioRxiv

28. 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., Nguyen, P. T., Ó Conchúir, S., Roy Burman, S. S., Samanta, R., Smith, S. T., Teets, F., Tiemann, J. K. S., 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, K., Meiler, J., Schief, W., Schueler-Furman, O., Siegel, J. B., Stein, A., Yarov-Yarovoy, V., Kuhlman, B., Leaver-Fay, A., Gront, D., Gray, J. J. & Bonneau, R. Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks. Nat. Commun. 2021, 121, 12, 1–15 (2021). https://doi.org/10.1038/s41467-021-27222-7. 1,700 reads and 91st percentile of ~300,000 articles of similar age within 2 weeks of publication.

27. Gligorijević, V., Renfrew, P. D., Kosciolek, T., Koehler Leman, J., Berenberg, D., Vatanen, T., Chandler, C., Taylor, B. C., Fisk, I. M., Vlamakis, H., Xavier, R. J., Knight, R., Cho, K. & Bonneau, R. Structure-based protein function prediction using graph convolutional networks. Nat. Commun. 2021 121 12, 1–14 (2021).

26. Koehler Leman J, Bonneau R Specificities of modeling membrane proteins using multi-template homology modeling. Accepted at Methods in Molecular Biology.

25. Koehler Leman, J., Weitzner, B. D., Lewis, S. M., Consortium, R. & Bonneau, R. Macromolecular Modeling and Design in Rosetta: New Methods and Frameworks. preprints.org (2020). doi:10.20944/PREPRINTS201904.0263.V1. Accepted at Nature Methods.

24. Koehler Leman, J., Weitzner, B. D., Renfrew, P. D., Lewis, S. M., Moretti, R., Watkins, A. M., Mulligan, V. K., Lyskov, S., Adolf-Bryfogle, J., Labonte, J. W., Consortium, R., Bystroff, C., Schief, W., Schueler-Furman, O., Baker, D., Bradley, P., Dunbrack, R., Kortemme, T., Leaver-Fay, A., Strauss, C. E., Meiler, J., Kuhlman, B., Gray, J. J. & Bonneau, R. Better together: Elements of successful scientific software development in distributed collaborative community. Accepted. PlosCompBio (2020).

23. Salazar, M. D., Zelt, N. B., Saldivar, R., Kuntz, C. P., Chen, S., Penn, W. D., Bonneau, R., Koehler Leman, J. & Schlebach, J. P. Classification of the Molecular Defects Associated with Pathogenic Variants of the SLC6A8 Creatine Transporter. Biochemistry 59, 1367–1377 (2020). [PDF]

22. Kuenze G, Bonneau R, Koehler Leman J, Meiler J (2019) Integrative Protein Modeling in RosettaNMR from Sparse Paramagnetic Restraints. Structure 27:1721-1734.e5. https://doi.org/10.1016/j.str.2019.08.012 [PDF]

21. Koehler Leman, J., Bonneau, R. & Ulmschneider, M. B. Statistically derived asymmetric membrane potentials from α-helical and β-barrel membrane proteins. Sci. Rep. 8, 4446 (2018). [PDF]

20. Glusman, G., Rose, P. W., Prlić, A., Dougherty, J., Duarte, J. M., Hoffman, A. S., Barton, G. J., Bendixen, E., Bergquist, T., Bock, C., Brunk, E., Buljan, M., Burley, S. K., Cai, B., Carter, H., Gao, J., Godzik, A., Heuer, M., Hicks, M., Hrabe, T., Karchin, R., Koehler Leman, J., Lane, L., Masica, D. L., Mooney, S. D., Moult, J., Omenn, G. S., Pearl, F., Pejaver, V., Reynolds, S. M., Rokem, A., Schwede, T., Song, S., Tilgner, H., Valasatava, Y., Zhang, Y. & Deutsch, E. W. Mapping genetic variations to three-dimensional protein structures to enhance variant interpretation: a proposed framework. Genome Med. 9, 113 (2017). [PDF]

19. Koehler Leman, J. & Bonneau, R. A novel domain assembly routine for creating full-length models of membrane proteins from known domain structures. Biochemistry acs.biochem.7b00995 (2017). doi:10.1021/acs.biochem.7b00995 [PDF]

Front cover of Biochemistry

18. Koehler Leman, J., D’Avino, A. R., Bhatnagar, Y., & Gray, J. J. (2017). Comparison of NMR and crystal structures of membrane proteins and computational refinement to improve model quality. Proteins: Structure, Function, and Bioinformatics. http://doi.org/10.1002/prot.25402 [PDF]

Back cover of Proteins

17. Leippe, P., Koehler Leman, J., & Trauner, D. (2017). Specificity and Speed: Tethered Photopharmacology. Biochemistry, 56(39), 5214–5220. http://doi.org/10.1021/acs.biochem.7b00687 [PDF]

16. H. Freedman, M. R. Logan, D. Hockman, J. Koehler Leman, J. L. M. Law, and M. Houghton, Computational prediction of the heterodimeric and higher order structure of gpE1/gpE2 envelope glycoproteins encoded by the hepatitis C virus (HCV)., J. Virol., p. JVI.02309-16, 2017. [PDF]

15. Koehler Leman, J., Lyskov, S., & Bonneau, R. (2017). Computing structure-based lipid accessibility of membrane proteins with mp_lipid_acc in RosettaMP. BMC Bioinformatics, 18(1), 115. http://doi.org/10.1186/s12859-017-1541-z [PDF]

14. J. Koehler Leman, B. K. Mueller, and J. J. Gray, Expanding the toolkit for membrane protein modeling in Rosetta, Bioinformatics, vol. 11, pp. 1–3, Dec. 2016. [PDF]

13. Finn, J. A., Koehler Leman, J., Willis, J. R., Cisneros, A., Crowe, J. E. & Meiler, J. Improving Loop Modeling of the Antibody Complementarity-Determining Region 3 Using Knowledge-Based Restraints. PLoS One 11, e0154811 (2016). [PDF]

12. D Lokits, A., Koehler Leman, J., E Kitko, K., S Alexander, N., E Hamm, H. & Meiler, J. A survey of conformational and energetic changes in G protein signaling. AIMS Biophys. 2, 630–648 (2015). [PDF]

11. Braun, T., Koehler Leman, J. & Lange, O. F. Combining Evolutionary Information and an Iterative Sampling Strategy for Accurate Protein Structure Prediction. PLoS Comput. Biol. 11, 1–20 (2015). [PDF]

10. Alford, R. F., Koehler Leman, J., Weitzner, B. D., Duran, A. M., Tilley, D. C., Elazar, A. & Gray, J. J. An Integrated Framework Advancing Membrane Protein Modeling and Design. PLoS Comput. Biol. 11, e1004398 (2015). [PDF] - *co-first-authors

9. Ulmschneider, M. B., Koehler Leman, J., Fennell, H. & Beckstein, O. Peptide Folding in Translocon-Like Pores. J. Membr. Biol. 248, 407–17 (2015). [PDF]

8. Pilla, K. B., Koehler Leman, J., Otting, G. & Huber, T. Capturing conformational States in proteins using sparse paramagnetic NMR data. PLoS One 10, e0127053 (2015). [PDF]

7. Koehler Leman, J., Ulmschneider, M. B. & Gray, J. J. Computational modeling of membrane proteins. Proteins Struct. Funct. Bioinforma. 83, 1–24 (2015). [PDF]

6. Koehler Leman, J., Mueller, R., Karakas, M., Woetzel, N. & Meiler, J. Simultaneous prediction of protein secondary structure and transmembrane spans. Proteins 81, 1127–40 (2013). [PDF]

5. Koehler, J. & Meiler, J. Expanding the utility of NMR restraints with paramagnetic compounds: background and practical aspects. Prog. Nucl. Magn. Reson. Spectrosc. 59, 360–89 (2011). [PDF]

4. Koehler, J., Sulistijo, E. S., Sakakura, M., Kim, H. J., Ellis, C. D. & Sanders, C. R. Lysophospholipid micelles sustain the stability and catalytic activity of diacylglycerol kinase in the absence of lipids. Biochemistry 49, 7089–99 (2010). [PDF]

3. Koehler, J., Woetzel, N., Staritzbichler, R., Sanders, C. R. & Meiler, J. A unified hydrophobicity scale for multispan membrane proteins. Proteins Struct. Funct. Bioinforma. 76, 13–29 (2009). [PDF]

2. Koehler, J., Mueller, R. & Meiler, J. Improved prediction of trans-membrane spans in proteins using an artificial neural network. in 2009 IEEE Symp. Comput. Intell. Bioinforma. Comput. Biol. 68–74 (IEEE, 2009). doi:10.1109/CIBCB.2009.4925709 [PDF]

1. Reuther, G., Tan, K.-T., Köhler, J., Nowak, C., Pampel, A., Arnold, K., Kuhlmann, J., Waldmann, H. & Huster, D. Structural model of the membrane-bound C terminus of lipid-modified human N-ras protein. Angew. Chem. Int. Ed. Engl. 45, 5387–90 (2006). [PDF]

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