Theoretische Chemie, Ruhr-Universität Bochum Up

Publications of Lars Schäfer and the Molecular Simulation Group

Publications in Peer-Reviewed Journals

36.    O. Fisette, C. Päslack, R. Barnes, J. M. Isas, R. Langen, M. Heyden, S. Han, L. V. Schäfer. Hydration Dynamics of a Peripheral Membrane Protein, submitted
35.    K. Reichel, O. Fisette, T. Braun, O. F. Lange, G. Hummer, L. V. Schäfer. Systematic evaluation of CS-Rosetta for membrane protein structure prediction with sparse NOE restraints, submitted
34.    M. Prieß, L. V. Schäfer. Release of Entropic Spring Reveals Conformational Coupling Mechanism in the ABC Transporter BtuCD-F, Biophys. J., 2016, 110, 2407-2418. (doi)
33.    O. Fisette, S. Wingbermühle, R. Tampé, L. V. Schäfer. Molecular Mechanism of Peptide Editing in the Tapasin-MHC I Complex, Sci. Rep., 2016, 6, 19085. (doi)
32.    A. Blees, K. Reichel, S. Trowitzsch, O. Fisette, C. Bock, R. Abele, G. Hummer, L. V. Schäfer, R. Tampé. Assembly of the MHC I Peptide-Loading Complex Determined by a Conserved Ionic Lock-Switch, Sci. Rep., 2015, 5, 17341. (doi)
31.    G. Fleischmann, O. Fisette, C. Thomas, R. Wieneke, F. Tumulka, C. Schneeweiss, S. Springer, L. V. Schäfer, R. Tampé. Mechanistic Basis for Epitope Proofreading in the Peptide Loading Complex, J. Immunol., 2015, 195 (9), 4503-4513. (doi) See also "In This Issue" highlight in The Journal of Immunology.
30.    A. B. Kuhn, S. M. Gopal, L. V. Schäfer. On Using Atomistic Solvent Layers in Hybrid All-Atom/Coarse-Grained Molecular Dynamics Simulations, J. Chem. Theory Comput., 2015, 11 (9), 4460-4472. (doi)
29.    A. Debnath, L. V. Schäfer. Structure and Dynamics of Phospholipid Nanodiscs from All-Atom and Coarse-Grained Simulations, J. Phys. Chem. B, 2015, 119 (23), 6991-7002. (doi)
28.    S. M. Gopal, A. B. Kuhn, L. V. Schäfer. Systematic Evaluation of Bundled SPC Water for Biomolecular Simulations, Phys. Chem. Chem. Phys., 2015, 17, 8393-8406. (doi)
27.    S. Eggensperger, O. Fisette, D. Parcej, L. V. Schäfer, R. Tampé. An Annular Lipid Belt is Essential for Allosteric Coupling and Viral Inhibition of the Antigen Translocation Complex TAP, J. Biol. Chem., 2014, 289 (48), 33098-33108. (doi) COVER
26.    P. Lloris-Garcera, J. S. Slusky, S. Seppälä, M. Prieß, L. V. Schäfer, G. von Heijne. In vivo Trp-Scanning of the Small Multidrug Resistance Protein EmrE Confirms 3D Structure Models, J. Mol. Biol., 2013, 425 (22), 4642-4651. (doi)
25.    M. Majsnerowska, I. Hänelt, D. Wunnicke, L. V. Schäfer, H.-J. Steinhoff, D. J. Slotboom. Substrate-induced Conformational Changes in the S-component ThiT from an Energy Coupling Factor Transporter, Structure, 2013, 21 (5), 861-867. (doi)
24.    T. A. Wassenaar, H. I. Ingolfsson, M. Prieß, S. J. Marrink, L. V. Schäfer. Mixing Martini: Electrostatic Coupling in Hybrid Atomistic/Coarse-Grained Biomolecular Simulations, J. Phys. Chem. B, 2013, 117 (13), 3516-3530. (doi) COVER
23.    D. H. de Jong, G. Singh, W. F. D. Bennett, C. Arnarez, T. A. Wassenaar, L. V. Schäfer, X. Periole, D. P. Tieleman, and S. J. Marrink. Improved Parameters For The Martini Coarse-Grained Protein Force Field, J. Chem. Theory Comput., 2013, 9, 687-697. (doi)
22.    J. Domanski, S. J. Marrink, L. V. Schäfer. Transmembrane Helices can Induce Domain Formation in Crowded Model Membranes, Biochim. Biophys. Acta - Biomembr., 2012, 1818 (4), 984-994. (doi)
21.    A. Kazaryan, Z. Lan. L. V. Schäfer, W. Thiel, M. Filatov. Surface Hopping Excited-State Dynamics Study of the Photoisomerization of a Light-Driven Fluorene Molecular Rotary Motor, J. Chem. Theory Comput., 2011, 7 (7), 2189-2199. (doi)
20.    D. H. de Jong, L. V. Schäfer, A. H. de Vries, S. J. Marrink, H. J. C. Berendsen, H. Grubmüller. Determining Equilibrium Constants for Dimerization Reactions from Molecular Dynamics Simulations, J. Comput. Chem., 2011, 32 (9), 1919-1928. (doi)
19.    L. V. Schäfer, D. H. de Jong, A. Holt, A. J. Rzepiela, A. H. de Vries, B. Poolman, J. A. Killian, S. J. Marrink. Lipid Packing Drives the Segregation of Transmembrane Helices into Disordered Lipid Domains in Model Membranes, Proc. Natl. Acad. Sci. USA, 2011, 108 (4), 1343-1348. (doi)
18.    L. V. Schäfer, S. J. Marrink. Partitioning of Lipids at Domain Boundaries in Model Membranes, Biophys. J., 2010, 99 (12), L91-L93. (doi)
17.    S. Ramadurai, A. Holt, L. V. Schäfer, V. V. Krasnikov, D. T. S. Rijkers, S. J. Marrink, J. A. Killian, B. Poolman. Influence of Hydrophobic Mismatch and Amino Acid Composition on the Lateral Diffusion of Transmembrane Peptides, Biophys. J., 2010, 99 (5), 1447-1454. (doi)
16.    N. Kucerka, D. Marquardt, T. A. Harroun, M. P. Nieh, S. R. Wassall, D. H. de Jong, L. V. Schäfer, S. J. Marrink, J. Katsaras. Cholesterol in Bilayers with PUFA Chains: Doping with DMPC or POPC Results in Sterol Reorientation and Membrane-Domain Formation, Biochemistry, 2010, 49 (35), 7485-7493. (doi)
15.    S. O. Yesylevskyy, L. V. Schäfer, D. Sengupta, S. J. Marrink. Polarizable Water Model for the Coarse-Grained MARTINI Force Field, PLoS Comput. Biol., 2010, 6 (6), e1000810. (doi)
14.    A. J. Rzepiela, L. V. Schäfer, N. Goga, H. J. Risselada, A. H. de Vries, S. J. Marrink. Reconstruction of Atomistic Details from Coarse-Grained Structures, J. Comput. Chem., 2010, 31 (6), 1333-1343. (doi)
13.    A. Kazaryan, J. C. M. Kistemaker, L. V. Schäfer, W. R. Browne, B. L. Feringa, M. Filatov. Understanding the Dynamics Behind the Photoisomerization of a Light-Driven Fluorene Molecular Rotary Motor, J. Phys. Chem. A, 2010, 114 (15), 5058–5067. (doi)
12.    G. Groenhof, M. Boggio-Pasqua, L. V. Schäfer, M. A. Robb. Computer Simulations of Photobiological Processes: The Effect of the Protein Environment, Advances in Quantum Chemistry, 2010, 59, 181-212. (doi)
11.    L. V. Schäfer, G. Groenhof, M. Boggio-Pasqua, M. A. Robb, H. Grubmüller. Chromophore Protonation State controls Photoswitching of the Fluoroprotein asFP595, PLoS Comput. Biol., 2008, 4 (3), e1000034. (doi)
10.    E. M. Puchner, A. Alexandrovich, A. L. Kho, U. Hensen, L. V. Schäfer, B. Brandmeier, F. Gräter, H. Grubmüller, H. E. Gaub, M. Gautel. Mechanoenzymatics of Titin Kinase, Proc. Natl. Acad. Sci. USA, 2008, 105, 13385-13390. (doi)
  9.    G. Groenhof, L. V. Schäfer, M. Boggio-Pasqua, H. Grubmüller, M. A. Robb. Arginine52 Controls the Photoisomerization Process in Photoactive Yellow Protein, J. Am. Chem. Soc., 2008, 130, 3250-3251. (doi)
  8.    M. Boggio-Pasqua, G. Groenhof, L. V. Schäfer, H. Grubmüller, M. A. Robb. Ultrafast Deactivation Channel for Thymine Dimerization, J. Am. Chem. Soc., 2007, 129, 10996-10997. (doi)
  7.    G. Groenhof, L. V. Schäfer, M. Boggio-Pasqua, M. Goette, H. Grubmüller, M. A. Robb. Ultrafast Deactivation of an Excited Cytosine-Guanine Base Pair in DNA, J. Am. Chem. Soc., 2007, 129, 6812-6819. (doi)
  6.    L. V. Schäfer, E. M. Müller, H. E. Gaub, H. Grubmüller. Elastic Properties of Photoswitchable Azobenzene Polymers from Molecular Dynamics Simulations. Angew. Chemie int. Ed., 2007, 46, 2232-2237. (doi)
  5.    L. V. Schäfer, G. Groenhof, A. R. Klingen, G. M. Ullmann, M. Boggio-Pasqua, M. A. Robb, H. Grubmüller. Photoswitching of the Fluorescent Protein asFP595: Mechanism, Proton Pathways, and Absorption Spectra. Angew. Chemie int. Ed., 2007, 46, 530-536. (doi)
  4.    O. F. Lange, L. V. Schäfer, H. Grubmüller. Flooding in GROMACS: Accelerated Barrier Crossings in Molecular Dynamics. J. Comput. Chem., 2006, 27, 1693-1702. (doi)
  3.    M. Andresen, M. C. Wahl, A. C. Stiel, F. Gräter, L. V. Schäfer, S. Trowitzsch, G. Weber, C. Eggeling, H. Grubmüller, S. W. Hell, S. Jakobs. Structure and Mechanism of the Reversible Photoswitch of a Fluorescent Protein. Proc. Natl. Acad. Sci. USA, 2005, 102, 13070-13074. (doi)
  2.    A. Chichinin, T. S. Einfeld, K.-H. Gericke, J. Grunenberg, C. Maul, L. V. Schäfer. Photodissociation Dynamics of SOCl2. Phys. Chem. Chem. Phys., 2005, 7, 301-309. (doi)
  1.    L. Schäfer, N. Gödecke, O. Ott, C. Maul, K.-H. Gericke, P. S. Shternin, E. V. Orlenko, O. S. Vasyutinskii. Recoil velocity-dependent spin-orbit state distribution of chlorine photofragments. Chem. Phys., 2004, 301, 213-224. (doi)

Book Chapters, Lecture Notes

  2.    L. V. Schäfer. Coarse-Grain Water and Solutions: Hybrid AA/CG with Martini. In: Computational Trends in Solvation and Transport in Liquids, pp. 333-348. Editors: G. Sutmann, J. Grotendorst, G. Gompper, D. Marx. Lecture Notes of the Jülich CECAM School, Jülich Supercomputing Centre, March 2015. (download)
  1.    G. Groenhof, L. V. Schäfer, M. Boggio-Pasqua, M. A. Robb. Excited State Dynamics in Biomolecules. In: Handbook of Molecular Biophysics: Methods and Applications. Editor: H. G. Bohr. WILEY-VCH, 2009. ISBN: 978-3-527-40702-6

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