Publications of the Department (MPG.PuRe list)

Journal Article (27)

1.
Journal Article
Peng, B. Z.; Bock, L. V.; Belardinelli, R.; Peske, F.; Grubmüller, H.; Rodnina, M. V.: Active role of elongation factor G in maintaining the mRNA reading frame during translation. Science Advances 5 (12), eaax8030 (2019)
2.
Journal Article
Elisee, E.; Gapsys, V.; Mele, N.; Chaput, L.; Selwa, E.; de Groot, B. L.; Iorga, B. I.: Performance evaluation of molecular docking and free energy calculations protocols using the D3R Grand Challenge 4 dataset. Journal of Computer-Aided Molecular Design 33, pp. 1031 - 1043 (2019)
3.
Journal Article
Kopec, W.; Rothberg, B. S.; de Groot, B. L.: Molecular mechanism of a potassium channel gating through activation gate-selectivity filter coupling. Nature Communications 10, 5366 (2019)
4.
Journal Article
Lapolla, A.; Godec, A.: Manifestations of projection-induced memory: General theory and the tilted single file. Frontiers in Physics 7, 182 (2019)
5.
Journal Article
Kutzner, C.; Páll, S.; Fechner, M.; Esztermann, A.; de Groot, B. L.; Grubmüller, H.: More bang for your buck: Improved use of GPU nodes for GROMACS 2018. Journal of Computational Chemistry 40 (27), pp. 2418 - 2431 (2019)
6.
Journal Article
Bock, L. V.; Caliskan, N.; Korniy, N.; Peske, F.; Rodnina, M. V.; Grubmüller, H.: Thermodynamic control of −1 programmed ribosomal frameshifting. Nature Communications 10, 4598 (2019)
7.
Journal Article
Nagy, G.; Igaev, M.; Hoffmann, S. V.; Jones, N. C.; Grubmüller, H.: SESCA: Predicting circular dichroism spectra from protein molecular structures. Journal of Chemical Theory and Computation 15 (9), pp. 5087 - 5102 (2019)
8.
Journal Article
Aldeghi, M.; Gapsys, V.; de Groot, B. L.: Predicting kinase inhibitor resistance: Physics-based and data-driven approaches. ACS Central Science 5 (8), pp. 1468 - 1474 (2019)
9.
Journal Article
Öster, C.; Hendriks, K.; Kopec, W.; Chevelkov, V.; Shi, C.; Michl, D.; Lange, S.; Sun, H.; de Groot, B. L.; Lange, A.: The conduction pathway of potassium channels is water free under physiological conditions. Science Advances 5 (7), eaaw6756 (2019)
10.
Journal Article
Gapsys, V.; de Groot, B. L.: Comment on 'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size'. eLife 8, e44718 (2019)
11.
Journal Article
Hartich, D.; Godec, A.: Extreme value statistics of ergodic Markov processes from first passage times in the large deviation limit. Journal of Physics A: Mathematical and Theoretical 52, 244001 (2019)
12.
Journal Article
Coci, E. G.; Gapsys, V.; Shur, N.; Shin‐Podskarbi, Y.; de Groot, B.; Miller, K.; Vockley, J.; Sondheimer, N.; Ganetzky, R.; Freisinger, P.: Pyruvate carboxylase deficiency type A and type C: Characterization of 5 novel pathogenic variants in PC and analysis of the genotype-phenotype correlation. Human Mutation 40 (6), pp. 816 - 827 (2019)
13.
Journal Article
Song, C.; de Groot, B. L.; Sansom, M. S. P.: Lipid bilayer composition influences the activity of the antimicrobial peptide dermcidin channel. Biophysical Journal 116 (9), pp. 1658 - 1666 (2019)
14.
Journal Article
Rico, F.; Russek, A.; Gonzalez, L.; Grubmüller, H.; Scheuring, S.: Heterogeneous and rate-dependent streptavidin-biotin unbinding revealed by high-speed force spectroscopy and molecular dynamics simulations. Proceedings of the National Academy of Sciences of the United States of America 116 (14), pp. 6594 - 6601 (2019)
15.
Journal Article
Rico, F.; Russek, A.; González, L.; Grubmüller, H.; Scheuring, S.: Heterogeneous and rate-dependent streptavidin–biotin unbinding revealed by high-speed force spectroscopy and atomistic simulations. Proceedings of the National Academy of Sciences of the United States of America 116 (14), pp. 6594 - 6601 (2019)
16.
Journal Article
Igaev, M.; Kutzner, C.; Bock, L. V.; Vaiana, A. C.; Grubmüller, H.: Automated cryo-EM structure refinement using correlation-driven molecular dynamics. eLife 8, e43542 (2019)
17.
Journal Article
Hartich, D.; Godec, A.: Interlacing relaxation and first-passage phenomena in reversible discrete and continuous space Markovian dynamics. Journal of Statistical Mechanics: Theory and Experiment 2019, 024002 (2019)
18.
Journal Article
Yee, A. W.; Aldeghi, M.; Blakeley, M. P.; Ostermann, A.; Mas, P. J.; Moulin, M.; de Sanctis, D.; Bowler, M. W.; Mueller-Dieckmann, C.; Mitchell, E. P. et al.; Haertlein, M.; de Groot, B. L.; Boeri Erba, E.; Forsyth, V. T.: A molecular mechanism for transthyretin amyloidogenesis. Nature Communications 10 (1), 925 (2019)
19.
Journal Article
Schewe, M.; Sun, H.; Mert, Ü.; Mackenzie, A.; Pike, A. C. W.; Schulz, F.; Constantin, C.; Vowinkel, K. S.; Conrad, L. J.; Kiper, A. K. et al.; Gonzalez, W.; Musinszki, M.; Tegtmeier, M.; Pryde, D. C.; Belabed, H.; Nazare, M.; de Groot, B. L.; Decher, N.; Fakler, B.; Carpenter, E. P.; Tucker, S. J.; Baukrowitz, T.: A pharmacological master key mechanism that unlocks the selectivity filter gate in K+ channels. Science 363 (6429), pp. 875 - 880 (2019)
20.
Journal Article
Awasthi, N.; Kopec, W.; Wilkosz, N.; Jamroz, D.; Hub, J. S.; Zatorska, M.; Petka, R.; Nowakowska, M.; Kepczynski, M.: Molecular mechanism of polycation-induced pore formation in biomembranes. ACS Biomaterials Science and Engineering 5 (2), pp. 780 - 794 (2019)
21.
Journal Article
Cordeiro, S.; Finol-Urdaneta, R. K.; Köpfer, D.; Markushina, A.; Song, J.; French, R. J.; Kopec, W.; de Groot, B. L.; Giacobassi, M. J.; Leavitt, L. S. et al.; Raghuraman, S.; Teichert, R. W.; Olivera, B. M.; Terlau, H.: Conotoxin κM-RIIIJ, a tool targeting asymmetric heteromeric Kv1 channels. Proceedings of the National Academy of Sciences of the United States of America 116 (3), pp. 1059 - 1064 (2019)
22.
Journal Article
Briones, R.; Blau, C.; Kutzner, C.; de Groot, B. L.; Aponte-Santamaría, C.: GROmaρs: A GROMACS-based toolset to analyze density maps derived from molecular dynamics simulations. Biophysical Journal 116 (1), pp. 4 - 11 (2019)
23.
Journal Article
Lutz, H.; Jaeger, V.; Weidner, T.; de Groot, B. L.: Interpretation of interfacial protein spectra with enhanced molecular simulation ensembles. Journal of Chemical Theory and Computation 15 (1), pp. 698 - 707 (2019)
24.
Journal Article
Abraham, M. J.; Apostolov, R. P.; Barnoud, J.; Bauer, P.; Blau, C.; Bonvin, A. M. J. J.; Chavent, M.; Chodera, J. D.; Čondić-Jurkić, K.; Delemotte, L. et al.; Grubmüller, H.; Howard, R. J.; Jordan, E. J.; Lindal, E.; Ollila, O. H. S.; Selent, J.; Smith, D. G. A.; Stansfeld, P. J.; Tiemann, J. K. S.; Trellet, M.; Woods, C. J.; Zhmurov, A.: Sharing data from molecular simulations. Journal of Chemical Information and Modeling 59 (10), pp. 4093 - 4099 (2019)
25.
Journal Article
Gu, R. X.; Baoukina, S.; Tieleman, D. P.: Cholesterol flip-flop in heterogeneous membranes. Journal of Chemical Theory and Computation 15 (3), pp. 2064 - 2070 (2019)
26.
Journal Article
Paul, F.; Wu, H.; Vossel, M.; de Groot, B. L.; Noé, F.: Identification of kinetic order parameters for non-equilibrium dynamics. The Journal of Chemical Physics 150 (16), 164120 (2019)
27.
Journal Article
Rovo, P.; Smith, C. A.; Gauto, D.; de Groot, B. L.; Schanda, P.; Linser, R.: Mechanistic insights into microsecond time-scale motion of solid proteins using complementary 15N and 1H relaxation dispersion techniques. Journal of the American Chemical Society 141 (2), pp. 858 - 869 (2019)

Book Chapter (1)

28.
Book Chapter
Aldeghi, M.; de Groot, B. L.; Gapsys, V.: Accurate calculation of free energy changes upon amino acid mutation. In: Computational Methods in Protein Evolution, pp. 19 - 47 (Ed. Sikosek, T.). Springer Nature, New York (2019)
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