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Page 1
Bringing Molecular Dynamics Simulation Data into View.
Hildebrand PW, Rose AS, Tiemann JKS. Hildebrand PW, et al. Among authors: tiemann jks. Trends Biochem Sci. 2019 Nov;44(11):902-913. doi: 10.1016/j.tibs.2019.06.004. Epub 2019 Jul 10. Trends Biochem Sci. 2019. PMID: 31301982 Free article. Review.
Sharing Data from Molecular Simulations.
Abraham M, Apostolov R, Barnoud J, Bauer P, Blau C, Bonvin AMJJ, Chavent M, Chodera J, Čondić-Jurkić K, Delemotte L, Grubmüller H, Howard RJ, Jordan EJ, Lindahl E, Ollila OHS, Selent J, Smith DGA, Stansfeld PJ, Tiemann JKS, Trellet M, Woods C, Zhmurov A. Abraham M, et al. Among authors: tiemann jks. J Chem Inf Model. 2019 Oct 28;59(10):4093-4099. doi: 10.1021/acs.jcim.9b00665. Epub 2019 Oct 11. J Chem Inf Model. 2019. PMID: 31525920
GPCRmd uncovers the dynamics of the 3D-GPCRome.
Rodríguez-Espigares I, Torrens-Fontanals M, Tiemann JKS, Aranda-García D, Ramírez-Anguita JM, Stepniewski TM, Worp N, Varela-Rial A, Morales-Pastor A, Medel-Lacruz B, Pándy-Szekeres G, Mayol E, Giorgino T, Carlsson J, Deupi X, Filipek S, Filizola M, Gómez-Tamayo JC, Gonzalez A, Gutiérrez-de-Terán H, Jiménez-Rosés M, Jespers W, Kapla J, Khelashvili G, Kolb P, Latek D, Marti-Solano M, Matricon P, Matsoukas MT, Miszta P, Olivella M, Perez-Benito L, Provasi D, Ríos S, R Torrecillas I, Sallander J, Sztyler A, Vasile S, Weinstein H, Zachariae U, Hildebrand PW, De Fabritiis G, Sanz F, Gloriam DE, Cordomi A, Guixà-González R, Selent J. Rodríguez-Espigares I, et al. Among authors: tiemann jks. Nat Methods. 2020 Aug;17(8):777-787. doi: 10.1038/s41592-020-0884-y. Epub 2020 Jul 13. Nat Methods. 2020. PMID: 32661425
MDsrv: visual sharing and analysis of molecular dynamics simulations.
Kampfrath M, Staritzbichler R, Hernández GP, Rose AS, Tiemann JKS, Scheuermann G, Wiegreffe D, Hildebrand PW. Kampfrath M, et al. Among authors: tiemann jks. Nucleic Acids Res. 2022 Jul 5;50(W1):W483-W489. doi: 10.1093/nar/gkac398. Nucleic Acids Res. 2022. PMID: 35639717 Free PMC article.
Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks.
Koehler Leman J, Lyskov S, Lewis SM, Adolf-Bryfogle J, Alford RF, Barlow K, Ben-Aharon Z, Farrell D, Fell J, Hansen WA, Harmalkar A, Jeliazkov J, Kuenze G, Krys JD, Ljubetič A, Loshbaugh AL, Maguire J, Moretti R, Mulligan VK, Nance ML, Nguyen PT, Ó Conchúir S, Roy Burman SS, Samanta R, Smith ST, Teets F, Tiemann JKS, Watkins A, Woods H, Yachnin BJ, Bahl CD, Bailey-Kellogg C, Baker D, Das R, DiMaio F, Khare SD, Kortemme T, Labonte JW, Lindorff-Larsen K, Meiler J, Schief W, Schueler-Furman O, Siegel JB, Stein A, Yarov-Yarovoy V, Kuhlman B, Leaver-Fay A, Gront D, Gray JJ, Bonneau R. Koehler Leman J, et al. Among authors: tiemann jks. Nat Commun. 2021 Nov 29;12(1):6947. doi: 10.1038/s41467-021-27222-7. Nat Commun. 2021. PMID: 34845212 Free PMC article.
MDverse: Shedding Light on the Dark Matter of Molecular Dynamics Simulations.
Tiemann JKS, Szczuka M, Bouarroudj L, Oussaren M, Garcia S, Howard RJ, Delemotte L, Lindahl E, Baaden M, Lindorff-Larsen K, Chavent M, Poulain P. Tiemann JKS, et al. bioRxiv [Preprint]. 2023 May 2:2023.05.02.538537. doi: 10.1101/2023.05.02.538537. bioRxiv. 2023. PMID: 37205542 Free PMC article. Preprint.
Structural Insights into the Process of GPCR-G Protein Complex Formation.
Liu X, Xu X, Hilger D, Aschauer P, Tiemann JKS, Du Y, Liu H, Hirata K, Sun X, Guixà-González R, Mathiesen JM, Hildebrand PW, Kobilka BK. Liu X, et al. Among authors: tiemann jks. Cell. 2019 May 16;177(5):1243-1251.e12. doi: 10.1016/j.cell.2019.04.021. Epub 2019 May 9. Cell. 2019. PMID: 31080070 Free PMC article.
Publisher Correction: GPCRmd uncovers the dynamics of the 3D-GPCRome.
Rodríguez-Espigares I, Torrens-Fontanals M, Tiemann JKS, Aranda-García D, Ramírez-Anguita JM, Stepniewski TM, Worp N, Varela-Rial A, Morales-Pastor A, Medel-Lacruz B, Pándy-Szekeres G, Mayol E, Giorgino T, Carlsson J, Deupi X, Filipek S, Filizola M, Gómez-Tamayo JC, Gonzalez A, Gutiérrez-de-Terán H, Jiménez-Rosés M, Jespers W, Kapla J, Khelashvili G, Kolb P, Latek D, Marti-Solano M, Matricon P, Matsoukas MT, Miszta P, Olivella M, Perez-Benito L, Provasi D, Ríos S, R Torrecillas I, Sallander J, Sztyler A, Vasile S, Weinstein H, Zachariae U, Hildebrand PW, De Fabritiis G, Sanz F, Gloriam DE, Cordomi A, Guixà-González R, Selent J. Rodríguez-Espigares I, et al. Among authors: tiemann jks. Nat Methods. 2020 Aug;17(8):861-862. doi: 10.1038/s41592-020-0928-3. Nat Methods. 2020. PMID: 32704182
18 results