Publications of the group

2019

Petit, Dieter and Hitzenberger, Manuel and Lismont, Sam and Zoltowska, Katarzyna Marta and Ryan Natalie S. and Mercken, Mark and Bischoff, François and Zacharias, Marting and Chávez-Gutiérrez, Lucía, Extracellular interface between APP and Nicastrin regulates Ab length and response to c-secretase modulators, The EMBO journal, 2019, 38: e101494

Hitzenberger, Manuel and Zacharias, Martin, Uncovering the Binding Mode of γ -Secretase Inhibitors, ACS Chem. Neurosci. , 2019, 10(8), pp. 3398-3403

Hitzenberger, Manuel and Zacharias, Martin, Structural Modeling of γ-Secretase Aβn Complex Formation and Substrate Processing, ACS Chem. Neurosci., 2019, 10(3), pp. 1826-1840


Zacharias, Martin. "Atomic resolution insight on Sac7d protein binding to DNA and associated global changes by Molecular Dynamics Simulations." Angewandte Chemie (2019) 58(18):5967-5972.

Müller, S. I., Aschenbrenner, I., Zacharias, M., & Feige, M. J.  An Interspecies Analysis Reveals Molecular Construction Principles of Interleukin 27. Journal of molecular biology. 2019, S0022-2836(19)30239-6.

Kandzia, Florian, and Martin Zacharias. "Dynamics of the full-length yeast Hsp90 dimer." The European Physical Journal Special Topics 227.14 (2019): 1693-1704.

Samsonov, Sergey A., Martin Zacharias, and Isaure Chauvot de Beauchene. "Modeling large protein–glycosaminoglycan complexes using a fragment
based approach." Journal of computational chemistry (2019), 40(14):1429-1439.

Hitzenberger, Manuel, and Martin Zacharias. "Structural Modeling of
γ-Secretase Aβ n Complex Formation and Substrate Processing." ACS chemical neuroscience (2019) 10(3):1826-1840.

Siebenmorgen, Till, and Martin Zacharias. "Evaluation of predicted protein-protein complexes by binding free energy simulations." Journal of chemical theory and computation (2019) 15(3):2071-2086..

Reif, Maria, and Martin Zacharias. "Computer Modelling and Molecular Dynamics Simulation of Biomolecules." Biomolecular and Bioanalytical Techniques: Theory, Methodology and Applications (2019): 501-535.

Reif, Maria M. and Fischer, Moritz and Fredriksson, Kai and Hagn, Franz and Zacharias, Martin, The N-Terminal Segment of the Voltage-Dependent Anion Channel: A Possible Membrane-Bound Intermediate in Pore Unbinding, Journal of Molecular Biology, 2019, 431, pp. 223--243.

Müller, Stephanie I., et al. "A folding switch regulates interleukin 27 biogenesis and secretion of its α-subunit as a cytokine." Proceedings of the National Academy of Sciences (2019), 116(5):1585-1590.

Schindler, Christina EM, et al. "Free energy calculations elucidate substrate binding, gating mechanism, and tolerance
promoting mutations in herbicide target 4hydroxyphenylpyruvate dioxygenase." Protein Science (2019), 28(6):1048-1058.

2018

 

Schickinger, Matthias, Martin Zacharias, and Hendrik Dietz. "Tethered multifluorophore motion reveals equilibrium transition kinetics of single DNA double helices." Proceedings of the National Academy of Sciences 115.32 2018, E7512-E7521.

Hitzenberger, Manuel, and Martin Zacharias. "
γ-Secretase Studied by Atomistic Molecular Dynamics Simulations: Global Dynamics, Enzyme Activation, Water Distribution and Lipid Binding." Frontiers in Chemistry 6 ,2018, 640.


Weber, Benedikt and Brandl, Matthias J. and Pulido Cendales, María Daniela and Berner, Carolin and Pradhan, Tejaswini and Feind, Gina Maria and Zacharias, Martin and Reif, Bernd and Buchner, Johannes A single residue switch reveals principles of antibody domain integrity. Journal of Biological Chemistry, 2018, 293, pp. 17107--17118.

Spanopoulou, Anna and Heidrich, Luzia and Chen, Hong-Ru and Frost, Christina and Hrle, Dean and Malideli, Eleni and Hille, Kathleen and Grammatikopoulos, Alexandros and Bernhagen, Jürgen and Zacharias, Martin and Rammes, Gerhard and Kapurniotu, Aphrodite, Designed Macrocyclic Peptides as Nanomolar Amyloid Inhibitors Based on Minimal Recognition Elements. Angew. Chem. Int. Ed., 2018, 57, pp. 14503--14508.

Podewin, Tom and Broichhagen, Johannes and Frost, Christina and Groneberg, Dieter and Ast, Julia and Meyer-Berg, Helena and Fine, Nicholas H F and Friebe, And reas and Zacharias, Martin and Hodson, David J and Trauner, Dirk and Hoffmann-Röder, Anja, Optical control of a receptor-linked guanylyl cyclase using a photoswitchable peptidic hormone. Chemical science, 2017, 8, pp. 4644--4653.

Harrer, Nadine and Schindler, Christina E.M. and Bruetzel, Linda K. and Forné, Ignasi and Ludwigsen, Johanna and Imhof, Axel and Zacharias, Martin and Lipfert, Jan and Mueller-Planitz, Felix , Structural Architecture of the Nucleosome Remodeler ISWI Determined from Cross-Linking, Mass Spectrometry, SAXS, and Modeling. Structure, 2018, 26, pp. 282--294.

Liebl, Korbinian and Zacharias, Martin, How methyl-sugar interactions determine DNA structure and flexibility. Nucleic Acids Research, 2018, pp. gky1237--gky1237

Kriegel, Franziska and Matek, Christian and Dršata, Tomáš and Kulenkampff, Klara and Tschirpke, Sophie and Zacharias, Martin and Lankaš, Filip and Lipfert, Jan, The temperature dependence of the helical twist of DNA. Nucleic acids research, 2018, 46, pp. 7998--8009.

2017

Herold, Eva Maria and John, Christine and Weber, Benedikt and Kremser, Stephan and Eras, Jonathan and Berner, Carolin and Deubler, Sabrina and Zacharias, Martin and Buchner, Johannes
Determinants of the assembly and function of antibody variable domains. Scientific reports, 2017, 7, pp. 12276--12276.

Liebl, Korbinian and Zacharias, Martin, Unwinding Induced Melting of Double-Stranded DNA Studied by Free Energy Simulations. The Journal of Physical Chemistry B, 10, 2017, 121.

Luitz, Manuel P and Bomblies, Rainer and Zacharias, Martin, Comparative Molecular Dynamics Analysis of RNase-S Complex Formation. Biophysical journal, 2017, 113, pp. 1466--1474.

Bakou, Maria and Hille, Kathleen and Kracklauer, Michael and Spanopoulou, Anna and Frost, Christina V. and Malideli, Eleni and Yan, Li-Mei and Caporale, And rea and Zacharias, Martin and Kapurniotu, Aphrodite, Key aromatic/hydrophobic amino acids controlling a cross-amyloid peptide interaction versus amyloid self-assembly. Journal of Biological Chemistry, 2017, 292, pp. 14587-14602.

Zhang, Zhe and Ehmann, Uwe and Zacharias, Martin, Monte Carlo replica-exchange based ensemble docking of protein conformations. Proteins: Structure, Function, and Bioinformatics, 2017, 85, pp. 924--937.

Zeller, Fabian and Zacharias, Martin, Thermodynamics and Kinetics of Nucleobase Stacking Oligomerization revealed by Molecular Dynamics Simulations. Journal of Chemical Theory and Computation, 2017. ACS Publications (doi:10.1021/acs.jctc.7b00150)
 
Zacharias, Martin
Predicting allosteric changes from conformational ensembles
Structure, 2017, 25, pp. 393--394. Elsevier (doi:10.1016/j.str.2017.02.006)
 
de Vries, Sjoerd J and Rey, Julien and Schindler, Christina EM and Zacharias, Martin and Tuffery, Pierre
The pepATTRACT web server for blind, large-scale peptide--protein docking
Nucleic Acids Research, 2017. (doi:10.1093/nar/gkx335)
 
de Vries, Sjoerd J and Zacharias, Martin, Fast and accurate grid representations for atom-based docking with partner flexibility. Journal of Computational Chemistry, 2017, 38, pp. 1538--1546. Wiley Online Library (doi:10.1002/jcc.24795)
 
Siebenmorgen, Till and Zacharias, Martin, Origin of Ion Specificity of Telomeric DNA G-Quadruplexes Investigated by Free-Energy Simulations. Biophysical Journal, 2017, 112, pp. 2280--2290. Elsevier (doi:10.1016/j.bpj.2017.04.036)
 
Schwierz, Nadine and Frost, Christina V and Geissler, Phillip L and Zacharias, Martin
From Aß Filament to Fibril: Molecular Mechanism of Surface-Activated Secondary Nucleation from All-Atom MD Simulations. J. Phys. Chem. B, 2017, 121, pp. 671--682. ACS Publications (doi:10.1021/acs.jpcb.6b10189)
 
Schindler, Christina and Zacharias, Martin, Application of the ATTRACT Coarse-Grained Docking and Atomistic Refinement for Predicting Peptide-Protein Interactions. Modeling Peptide-Protein Interactions: Methods and Protocols, 2017, pp. 49--68. Springer (doi:10.1007/978-1-4939-6798-8_5)
 
Ostermeir, Katja and Zacharias, Martin, Accelerated flexible protein-ligand docking using Hamiltonian replica exchange with a repulsive biasing potential. PloS one, 2017, 12, pp. e0172072. Public Library of Science (doi:10.1371/journal.pone.0172072)
 
Luitz, Manuel P and Barth, And ers and Crevenna, Alvaro H and Bomblies, Rainer and Lamb, Don C and Zacharias, Martin, Covalent dye attachment influences the dynamics and conformational properties of flexible peptides. PloS one, 2017, 12, pp. e0177139. Public Library of Science (doi:10.1371/journal.pone.0177139)
 
Ludwigsen, Johanna and Pfennig, Sabrina and Singh, Ashish K and Schindler, Christina and Harrer, Nadine and Forné, Ignasi and Zacharias, Martin and Mueller-Planitz, Felix, Concerted regulation of ISWI by an autoinhibitory domain and the H4 N-terminal tail. eLife, 2017, 6, pp. e21477. eLife Sciences Publications Limited (doi:10.7554/elife.21477)
 
Knips, Alexander and Zacharias, Martin, Both DNA global deformation and repair enzyme contacts mediate flipping of thymine dimer damage. Scientific Reports, 2017, 7, pp. 41324.
 
Hellenkamp, Björn and Wortmann, Philipp and Kandzia, Florian and Zacharias, Martin and Hugel, Thorsten, Multidomain structure and correlated dynamics determined by self-consistent FRET networks. Nature methods, 2017, 14, pp. 174--180. Nature Research (doi:10.1038/nmeth.4081)
 
Chéron, Jean-Baptiste and Zacharias, Martin and Antonczak, Serge and Fiorucci, Sébastien
Update of the ATTRACT force field for the prediction of protein--protein binding affinity
Journal of Computational Chemistry, 2017. Wiley Online Library (doi:10.1002/jcc.24836)
 
Bomblies, Rainer and Luitz, Manuel Patrick and Scanu, Sandra and Madl, Tobias and Zacharias, Martin, Transient helicity in intrinsically disordered Axin-1 studied by NMR spectroscopy and molecular dynamics simulations. PloS one, 2017, 12, pp. e0174337. Public Library of Science (doi:10.1371/journal.pone.0174337)

2016

La Rosa, Giuseppe and Zacharias, Martin, Global deformation facilitates flipping of damaged 8-oxo-guanine and guanine in DNA. Nucleic Acids Res, Sep, 2016. (doi:10.1093/nar/gkw827)

Kilchherr, Fabian and Wachauf, Christian and Pelz, Benjamin and Rief, Matthias and Zacharias, Martin and Dietz, Hendrik, Single-molecule dissection of stacking forces in DNA. Science, Sep, 2016, 353. (doi:10.1126/science.aaf5508)

Häse, Florian and Zacharias, Martin, Free energy analysis and mechanism of base pair stacking in nicked DNA. Nucleic Acids Res, Sep, 2016, 44, pp. 7100--7108. (doi:10.1093/nar/gkw607)

Schindler, Christina EM and Chauvot de Beauchêne, Isaure and de Vries, Sjoerd and Zacharias, Martin, Protein-protein and peptide-protein docking and refinement using ATTRACT in CAPRI. Proteins: Structure, Function, and Bioinformatics, 2016. Wiley Online Library (doi:10.1002/prot.25196)

Szameit, Kristina and Berg, Katharina and Kruspe, Sven and Valentini, Erica and Magbanua, Eileen and Kwiatkowski, Marcel and {Chauvot de Beauchêne}, Isaure and Krichel, Boris and Schamoni, Kira and Uetrecht, Charlotte and Svergun, Dmitri I. and Schlüter, Hartmut and Zacharias, Martin and Hahn, Ulrich, Structure and target interaction of a G-quadruplex RNA-aptamer. RNA Biol, Oct, 2016, 13, pp. 973--987. (doi:10.1080/15476286.2016.1212151)

Nokwe, Cardine N. and Hora, Manuel and Zacharias, Martin and Yagi, Hisashi and Peschek, Jirka and Reif, Bernd and Goto, Yuji and Buchner, Johannes, A Stable Mutant Predisposes Antibody Domains to Amyloid Formation through Specific Non-Native Interactions. J Mol Biol, Mar, 2016, 428, pp. 1315--1332. (doi:10.1016/j.jmb.2016.01.015)

Luitz, Manuel P. and Bomblies, Rainer and Ramcke, Evelyn and Itzen, Aymelt and Zacharias, Martin, Adenylylation of Tyr77 stabilizes Rab1b GTPase in an active state: A molecular dynamics simulation analysis. Sci Rep, 2016, 6, pp. 19896. (doi:10.1038/srep19896)

Reif, Maria M. and Zacharias, Martin, Rapid approximate calculation of water binding free energies in the whole hydration domain of (bio)macromolecules. J Comput Chem, Jul, 2016, 37, pp. 1711--1724. (doi:10.1002/jcc.24390)

Schwierz, Nadine and Frost, Christina V. and Geissler, Phillip L. and Zacharias, Martin
Dynamics of Seeded A
β40-Fibril Growth from Atomistic Molecular Dynamics Simulations: Kinetic Trapping and Reduced Water Mobility in the Locking Step. J Am Chem Soc, Jan, 2016, 138, pp. 527--539. (doi:10.1021/jacs.5b08717)

Schwierz, Nadine and Krysiak, Stefanie and Hugel, Thorsten and Zacharias, Martin,
Mechanism of Reversible Peptide-Bilayer Attachment: Combined Simulation and Experimental Single-Molecule Study. Langmuir, Jan, 2016, 32, pp. 810--821. (doi:10.1021/acs.langmuir.5b03435)

Nokwe, Cardine N. and Hora, Manuel and Zacharias, Martin and Yagi, Hisashi and Peschek, Jirka and Reif, Bernd and Goto, Yuji and Buchner, Johannes, Specific non-native interactions. J Mol Biol, Jan, 2016. (doi:10.1016/j.jmb.2016.01.015)

Chauvot de Beauchene, Isaure and de Vries, Sjoerd J. and Zacharias, Martin, Binding Site Identification and Flexible Docking of Single Stranded RNA to Proteins Using a Fragment-Based Approach. PLoS Comput Biol, Jan, 2016, 12, pp. e1004697.  
doi:10.1371/journal.pcbi.1004697)

de Vries, Sjoerd J. and Chauvot de Beauchêne, Isaure and Schindler, Christina E M. and Zacharias, Martin, Cryo-EM Data Is Superior to Contact and Interface Information in Integrative Modeling. Biophys J, Feb, 2016. (doi:10.1016/j.bpj.2015.12.038)

Pelz, Benjamin and Žoldák, Gabriel and Zeller, Fabian and Zacharias, Martin and Rief, Matthias, Subnanometre enzyme mechanics probed by single-molecule force spectroscopy.
Nat Commun, Feb, 2016, 7, pp. 10848. (doi:10.1038/ncomms10848)

Bomblies, Rainer and Luitz, Manuel P and Zacharias, Martin, Molecular Dynamics Analysis of 4E-BP2 Protein Fold Stabilization Induced by Phosphorylation. The Journal of Physical Chemistry B, 2016. ACS Publications (doi:10.1021/acs.jpcb.6b08597)

Schindler, Christina E M. and {de Vries}, Sjoerd J. and Sasse, Alexander and Zacharias, Martin, SAXS Data Alone can Generate High-Quality Models of Protein-Protein Complexes.
Structure, Aug, 2016, 24, pp. 1387--1397. (doi:10.1016/j.str.2016.06.007)

Bomblies, Rainer and Luitz, Manuel P. and Zacharias, Martin, Mechanism of pKID/KIX Association Studied by Molecular Dynamics Free Energy Simulations. J. Phys. Chem. B, Aug, 2016, 120, pp. 8186--8192. American Chemical Society (ACS) (doi:10.1021/acs.jpcb.6b01792)

Schöppner, Patricia and Csaba, Gergely and Braun, Tatjana and Daake, Marina and Richter, Bettina and Lange, Oliver F. and Zacharias, Martin and Zimmer, Ralf and Haslbeck, Martin
Regulatory Implications of Non-Trivial Splicing: Isoform 3 of Rab1A Shows Enhanced Basal Activity and Is Not Controlled by Accessory Proteins. J Mol Biol, Apr, 2016, 428, pp. 1544--1557. (doi:10.1016/j.jmb.2016.02.028)

de Beauchene, Isaure Chauvot and de Vries, Sjoerd J. and Zacharias, Martin, Fragment-based modelling of single stranded RNA bound to RNA recognition motif containing proteins
Nucleic Acids Research, Apr, 2016, 44, pp. 4565--4580. Oxford University Press (OUP) (doi:10.1093/nar/gkw328)

2015

Zhang, Zhe and Schindler, Christina E M. and Lange, Oliver F. and Zacharias, Martin
Application of Enhanced Sampling Monte Carlo Methods for High-Resolution Protein-Protein Docking in Rosetta. PLoS One, 2015, 10, pp. e0125941. (doi:10.1371/journal.pone.0125941)

Zeller, Fabian and Zacharias, Martin, Substrate Binding Specifically Modulates Domain Arrangements in Adenylate Kinase. Biophysical Journal, Nov, 2015, 109, pp. 1978-1985. Elsevier BV (doi:10.1016/j.bpj.2015.08.049)

Nokwe, Cardine N. and Hora, Manuel and Zacharias, Martin and Yagi, Hisashi and John, Christine and Reif, Bernd and Goto, Yuji and Buchner, Johannes, The Antibody Light-Chain Linker Is Important for Domain Stability and Amyloid Formation. J Mol Biol, Nov, 2015, 427, pp. 3572--3586. (doi:10.1016/j.jmb.2015.09.012)

Mittelberger, Florian and Meyer, Cindy and Waetzig, Georg H. and Zacharias, Martin and Valentini, Erica and Svergun, Dmitri I. and Berg, Katharina and Lorenzen, Inken and Grötzinger, Joachim and Rose-John, Stefan and Hahn, Ulrich,RAID3--An interleukin-6 receptor-binding aptamer with post-selective modification-resistant affinity. RNA Biol, 2015, 12, pp. 1043--1053. (doi:10.1080/15476286.2015.1079681)

Manuel Luitz and Rainer Bomblies and Katja Ostermeir and Martin Zacharias, Exploring biomolecular dynamics and interactions using advanced sampling methods. Journal of Physics: Condensed Matter, 2015, 27, pp. 323101. (doi:10.1088/0953-8984/27/32/323101)

de Vries, Sjoerd J. and Schindler, Christina E M. and Chauvot de Beauchêne, Isaure and Zacharias, Martin, A Web Interface for Easy Flexible Protein-Protein Docking with ATTRACT.
Biophys J, Feb, 2015, 108, pp. 462-465. (doi:10.1016/j.bpj.2014.12.015)

Hocking, Henry G. and Häse, Florian and Madl, Tobias and Zacharias, Martin and Rief, Matthias and Žoldák, Gabriel, A compact native 24-residue supersecondary structure derived from the villin headpiece subdomain. Biophys J, Feb, 2015, 108, pp. 678--686. (doi:10.1016/j.bpj.2014.11.3482)

Liebl, Korbinian and Drsata, Tomas and Lankas, Filip and Lipfert, Jan and Zacharias, Martin
Explaining the striking difference in twist-stretch coupling between DNA and RNA: A comparative molecular dynamics analysis. Nucleic Acids Res, Dec, 2015, 43, pp. 10143--10156. (doi:10.1093/nar/gkv1028)

Cavasotto, Claudio N and Bomblies, Rainer and Luitz, Manuel and Zacharias, Martin, Free Energy Calculations of Ligand--Protein Binding. , 2015. CRC Press (doi:10.1201/b18799-15)

Boyer, Benjamin and Ezelin, Johann and Poulain, Pierre and Saladin, Adrien and Zacharias, Martin and Robert, Charles H. and Prévost, Chantal, An integrative approach to the study of filamentous oligomeric assemblies, with application to RecA. PLoS One, 2015, 10, pp. e0116414. (doi:10.1371/journal.pone.0116414)

Schindler, Christina E M. and {de Vries}, Sjoerd J. and Zacharias, Martin, Fully Blind Peptide-Protein Docking with pepATTRACT. Structure, Aug, 2015, 23, pp. 1507--1515. (doi:10.1016/j.str.2015.05.021)

Abualrous, Esam Tolba and Saini, Sunil Kumar and Ramnarayan, Venkat Raman and Ilca, Florin Tudor and Zacharias, Martin and Springer, Sebastian, The Carboxy Terminus of the Ligand Peptide Determines the Stability of the MHC Class I Molecule H-2Kb: A Combined Molecular Dynamics and Experimental Study. PLoS One, 2015, 10, pp. e0135421. (doi:10.1371/journal.pone.0135421)

2014

Zeller, Fabian and Zacharias, Martin, Efficient calculation of relative binding free energies by umbrella sampling perturbation. Journal of Computational Chemistry, Sep, 2014. Wiley-Blackwell (doi:10.1002/jcc.23744)

Ostermeir, Katja and Zacharias, Martin, Hamiltonian replica exchange combined with elastic network analysis to enhance global domain motions in atomistic molecular dynamics simulations. Proteins: Structure, Function, and Bioinformatics, Oct, 2014, 82, pp. 3410-3419. Wiley-Blackwell (doi:10.1002/prot.24695)

Kara, Mahmut and Drsata, Tomas and Lankas, Filip and Zacharias, Martin, Effect O6-guanine alkylation on DNA flexibility studied by comparative molecular dynamics simulations
Biopolymers, Oct, 2014, 103, pp. 23-32. Wiley-Blackwell (doi:10.1002/bip.22535)

Schindler, Christina E.M. and de Vries, Sjoerd J and Zacharias, Martin, iATTRACT: Simultaneous global and local interface optimization for protein-protein docking refinement
Proteins: Structure, Function, and Bioinformatics, Nov, 2014. Wiley-Blackwell (doi:10.1002/prot.24728)

Knips, Alexander and Zacharias, Martin, Influence of a cis, syn-cyclobutane pyrimidine dimer damage on DNA conformation studied by molecular dynamics simulations. Biopolymers, Nov, 2014. Wiley-Blackwell (doi:10.1002/bip.22586)

Saladin, Adrien and Rey, Julien and Thévenet, Pierre and Zacharias, Martin and Moroy, Gautier and Tufféry, Pierre, PEP-SiteFinder: a tool for the blind identification of peptide binding sites on protein surfaces. Nucleic Acids Res, May, 2014. (doi:10.1093/nar/gku404)

Luitz, Manuel and Zacharias, Martin, Protein-ligand docking using Hamiltonian replica exchange simulations with soft core potentials. J Chem Inf Model, May, 2014. (doi:10.1021/ci500296f)

Kannan, Srinivasaraghavan and Zacharias, Martin, Role of tryptophan side chain dynamics on the Trp-cage mini-protein folding studied by molecular dynamics simulations. PLoS One, 2014, 9, pp. e88383. (doi:10.1371/journal.pone.0088383)

Zeller, Fabian and Zacharias, Martin, Evaluation of Generalized Born Model Accuracy for Absolute Binding Free Energy Calculations. The Journal of Physical Chemistry B, Jun, 2014, pp. 140627155435006. American Chemical Society (ACS) (doi:10.1021/jp5015934)

Temme, Sebastian and Zacharias, Martin and Neumann, Jürgen and Wohlfromm, Sebastian and König, Angelika and Temme, Nadine and Springer, Sebastian and Trowsdale, John and Koch, Norbert, A novel family of human leukocyte antigen class II receptors may have its origin in archaic human species. J Biol Chem, Jan, 2014, 289, pp. 639--653. (doi:10.1074/jbc.M113.515767)

Ostermeir, Katja and Zacharias, Martin, Hamiltonian replica-exchange simulations with adaptive biasing of peptide backbone and side chain dihedral angles. J Comput Chem, Jan, 2014, 35, pp. 150--158. (doi:10.1002/jcc.23476)

Mishra, Sushil Kumar and Kara, Mahmut and Zacharias, Martin and Koca, Jaroslav
Enhanced conformational sampling of carbohydrates by Hamiltonian replica-exchange simulation. Glycobiology, Jan, 2014, 24, pp. 70--84. (doi:10.1093/glycob/cwt093)

Fiorucci, Sebastien and Zacharias, Martin, Computational Antigenic Epitope Prediction by Calculating Electrostatic Desolvation Penalties of Protein Surfaces Immunoinformatics, 2014, pp. 365-374. Springer Science + Business Media (doi:10.1007/978-1-4939-1115-8_20)

Zeller, Fabian and Zacharias, Martin, Adaptive Biasing Combined with Hamiltonian Replica Exchange to Improve Umbrella Sampling Free Energy Simulations. Journal of Chemical Theory and Computation, Feb, 2014, 10, pp. 703-710. American Chemical Society (ACS) (doi:10.1021/ct400689h)

Ostermeir, Katja and Springer, Sebastian and Zacharias, Martin, Coupling between side chain interactions and binding pocket flexibility in HLA-B*44:02 molecules investigated by molecular dynamics simulations. Molecular Immunology, Aug, 2014. Elsevier BV (doi:10.1016/j.molimm.2014.07.021)

Ostermeir, Katja and Zacharias, Martin, Rapid Alchemical Free Energy Calculation Employing a Generalized Born Implicit Solvent Model. The Journal of Physical Chemistry B, Aug, 2014. American Chemical Society (ACS) (doi:10.1021/jp506367y)

Nokwe, C. N. and Zacharias, M. and Yagi, H. and Hora, M. and Reif, B. and Goto, Y. and Buchner, J. A Residue-specific Shift in Stability and Amyloidogenicity of Antibody Variable Domains. Journal of Biological Chemistry, Aug, 2014, 289, pp. 26829-26846. American Society for Biochemistry & Molecular Biology (ASBMB) (doi:10.1074/jbc.m114.582247)

Lensink, Marc F. and Moal, Iain H. and Bates, Paul A. and Kastritis, Panagiotis L. and Melquiond, Adrien S J. and Karaca, Ezgi and Schmitz, Christophe and {van Dijk}, Marc and Bonvin, Alexandre M J J. and Eisenstein, Miriam and Jiménez-García, Brian and Grosdidier, Solène and Solernou, Albert and Pérez-Cano, Laura and Pallara, Chiara and Fernández-Recio, Juan and Xu, Jianqing and Muthu, Pravin and {Praneeth Kilambi}, Krishna and Gray, Jeffrey J. and Grudinin, Sergei and Derevyanko, Georgy and Mitchell, Julie C. and Wieting, John and Kanamori, Eiji and Tsuchiya, Yuko and Murakami, Yoichi and Sarmiento, Joy and Standley, Daron M. and Shirota, Matsuyuki and Kinoshita, Kengo and Nakamura, Haruki and Chavent, Matthieu and Ritchie, David W. and Park, Hahnbeom and Ko, Junsu and Lee, Hasup and Seok, Chaok and Shen, Yang and Kozakov, Dima and Vajda, Sandor and Kundrotas, Petras J. and Vakser, Ilya A. and Pierce, Brian G. and Hwang, Howook and Vreven, Thom and Weng, Zhiping and Buch, Idit and Farkash, Efrat and Wolfson, Haim J. and Zacharias, Martin and Qin, Sanbo and Zhou, Huan-Xiang and Huang, Shen-You and Zou, Xiaoqin and Wojdyla, Justyna A. and Kleanthous, Colin and Wodak, Shoshana J.
Blind prediction of interfacial water positions in CAPRI. Proteins, Apr, 2014, 82, pp. 620--632. (doi:10.1002/prot.24439)

2013

Saini, S. K. and Ostermeir, K. and Ramnarayan, V. R. and Schuster, H. and Zacharias, M. and Springer, S. Dipeptides promote folding and peptide binding of MHC class I molecules
Proceedings of the National Academy of Sciences, Sep, 2013, 110, pp. 15383-15388. Proceedings of the National Academy of Sciences (doi:10.1073/pnas.1308672110)

Dršata, Tomáš and Kara, Mahmut and Zacharias, Martin and Lankaš, Filip Effect of 8-Oxoguanine on DNA Structure and Deformability. J Phys Chem B, Sep, 2013. (doi:10.1021/jp407562t)

Despotovic, Dragana and Vojcic, Ljubica and Blanusa, Milan and Maurer, Karl-Heinz and Zacharias, Martin and Bocola, Marco and Martinez, Ronny and Schwaneberg, Ulrich,
Redirecting catalysis from proteolysis to perhydrolysis in subtilisin Carlsberg. Journal of Biotechnology, Sep, 2013, 167, pp. 279-286. Elsevier (doi:10.1016/j.jbiotec.2013.06.017)

Ostermeir, Katja and Zacharias, Martin, Advanced replica-exchange sampling to study the flexibility and plasticity of peptides and proteins. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, May, 2013, 1834, pp. 847-853. Elsevier (doi:10.1016/j.bbapap.2012.12.016)

Schütt, Antje and Zacharias, Martin and Schneider, Nico and Horn, Silke and Grötzinger, Joachim and Rose-John, Stefan and Schmidt-Arras, Dirk, gp130 activation is regulated by D2-D3 interdomain connectivity. Biochemical Journal, Mar, 2013, 450, pp. 487-496. Portland Press (doi:10.1042/BJ20121660)

Luitz, Manuel P. and Zacharias, Martin, Role of tyrosine hot-spot residues at the interface of colicin E9 and immunity protein 9: A comparative free energy simulation study. Proteins: Structure, Function, and Bioinformatics, Mar, 2013, 81, pp. 461-468. Wiley Blackwell (John Wiley & Sons) (doi:10.1002/prot.24203)

Kara, Mahmut and Zacharias, Martin, Influence of 8-Oxoguanosine on the Fine Structure of DNA Studied with Biasing-Potential Replica Exchange Simulations. Biophysical Journal, Mar, 2013, 104, pp. 1089-1097. Elsevier (doi:10.1016/j.bpj.2013.01.032)

Jankevicius, Gytis and Hassler, Markus and Golia, Barbara and Rybin, Vladimir and Zacharias, Martin and Timinszky, Gyula and Ladurner, Andreas G., A family of macrodomain proteins reverses cellular mono-{ADP}-ribosylation. Nature Structural \& Molecular Biology, Mar, 2013, 20, pp. 508-514. Nature Publishing Group (doi:10.1038/nsmb.2523)

Klähn, Marco and Zacharias, Martin, Transformations in plasma membranes of cancerous cells and resulting consequences for cation insertion studied with molecular dynamics. Physical Chemistry Chemical Physics, 2013, 15, pp. 14427. The Royal Society of Chemistry (doi:10.1039/c3cp52085d)

Kara, Mahmut and Zacharias, Martin, Stabilization of duplex DNA and RNA by dangling ends studied by free energy simulations. Biopolymers, 2013. (doi:10.1002/bip.22398)

Nuccitelli, Annalisa and Rinaudo, C. Daniela and Brogioni, Barbara and Cozzi, Roberta and Ferrer-Navarro, Mario and Yero, Daniel and Telford, John L. and Grandi, Guido and Daura, Xavier and Zacharias, Martin and et al. Understanding the Molecular Determinants Driving the Immunological Specificity of the Protective Pilus 2a Backbone Protein of Group B Streptococcus. PLoS Computational Biology, Jun, 2013, 9, pp. e1003115. Public Library of Science (doi:10.1371/journal.pcbi.1003115)

Steuten, Benedikt and Setny, Piotr and Zacharias, Martin and Wagner, Rolf, Mapping the Spatial Neighborhood of the Regulatory 6S RNA Bound to Escherichia coli RNA Polymerase Holoenzyme. Journal of Molecular Biology, Jul, 2013. Elsevier (doi:10.1016/j.jmb.2013.07.008)

Kara, Mahmut and Zacharias, Martin, Theoretical studies of nucleic acids folding. Wiley Interdisciplinary Reviews: Computational Molecular Science, Jul, 2013. Wiley Blackwell (John Wiley & Sons) (doi:10.1002/wcms.1146)

Zacharias, Martin, Combining coarse-grained nonbonded and atomistic bonded interactions for protein modeling. Proteins: Structure, Function, and Bioinformatics, Jan, 2013, 81, pp. 81-92. Wiley Blackwell (John Wiley & Sons) (doi:10.1002/prot.24164)

de Vries, Sjoerd and Zacharias, Martin, Flexible docking and refinement with a coarse-grained protein model using ATTRACT. Proteins: Structure, Function, and Bioinformatics, Aug, 2013. Wiley Blackwell (John Wiley & Sons) (doi:10.1002/prot.24400)

Uchtenhagen, Hannes and Abualrous, Esam T. and Stahl, Evi and Allerbring, Eva B. and Sluijter, Marjolein and Zacharias, Martin and Sandalova, Tatyana and van Hall, Thorbald and Springer, Sebastian and Nygren, Per-Ake and Achour, Adnane, Proline substitution independently enhances H-{2D} b complex stabilization and TCR recognition of melanoma-associated peptides. European Journal of Immunology, Aug, 2013, pp. n/a-n/a. Wiley Blackwell (John Wiley & Sons) (doi:10.1002/eji.201343456)

Bracher, Andreas and Kozany, Christian and Hähle, And reas and Wild, Philipp and Zacharias, Martin and Hausch, Felix, Crystal Structures of the Free and Ligand-Bound FK1-FK2 Domain Segment of FKBP52 Reveal a Flexible Inter-Domain Hinge. Journal of Molecular Biology, Aug, 2013. Elsevier (doi:10.1016/j.jmb.2013.07.041)

2012

Setny, Piotr and Bahadur, Ranjit and Zacharias, Martin, Protein-{DNA} docking with a coarse-grained force field. BMC Bioinformatics, 2012, 13, pp. 228. Springer (Biomed Central Ltd.) (doi:10.1186/1471-2105-13-228)

Schneider, Sebastian and Saladin, Adrien and Fiorucci, Sebastien and Prevost, Chantal and Zacharias, Martin, ATTRACT and PTOOLS: Open Source Programs for Protein-Protein Docking. Methods in Molecular Biology, 2012, 819, pp. 221-232. Springer New York (doi:10.1007/978-1-61779-465-0_15)

Leis, Simon and Zacharias, Martin, ReFlexIn: A Flexible Receptor Protein-Ligand Docking Scheme Evaluated on HIV-1 Protease. PLoS ONE, Oct, 2012, 7, pp. e48008. Public Library of Science (doi:10.1371/journal.pone.0048008)

Schneider, Sebastian and Zacharias, Martin,  Atomic resolution model of the antibody Fc interaction with the complement C1q component. Molecular Immunology, May, 2012, 51, pp. 66-72. Elsevier (doi:10.1016/j.molimm.2012.02.111)

Albu, Razvan F. and Zacharias, Martin and Jurkowski, Tomasz P. and Jeltsch, Albert
DNA Interaction of the CcrM DNA Methyltransferase: A Mutational and Modeling Study
ChemBioChem, Jun, 2012, 13, pp. 1304-1311. Wiley Blackwell (John Wiley & Sons) (doi:10.1002/cbic.201200082)

Schneider, Sebastian and Zacharias, Martin, Scoring optimisation of unbound protein-protein docking including protein binding site predictions. Journal of Molecular Recognition, Jan, 2012, 25, pp. 15-23. Wiley Blackwell (John Wiley & Sons) (doi:10.1002/jmr.1165)

de Vries, Sjoerd J. and Zacharias, Martin, ATTRACT-EM: A New Method for the Computational Assembly of Large Molecular Machines Using Cryo-EM Maps. PLoS ONE, Dec, 2012, 7, pp. e49733. Public Library of Science (doi:10.1371/journal.pone.0049733)

Schneider, Sebastian and Zacharias, Martin, Combining geometric pocket detection and desolvation properties to detect putative ligand binding sites on proteins. Journal of Structural Biology, Dec, 2012, 180, pp. 546-550. Elsevier (doi:10.1016/j.jsb.2012.09.010)

2011

Kannan, S. and Zacharias, M. Role of the closing base pair for d(GCA) hairpin stability: free energy analysis and folding simulations. Nucleic Acids Research, Oct, 2011, 39, pp. 8271-8280. Oxford University Press (doi:10.1093/nar/gkr541)

Setny, P. and Zacharias, M. A coarse-grained force field for Protein-RNA docking. Nucleic Acids Research, Nov, 2011, 39, pp. 9118-9129. Oxford University Press (doi:10.1093/nar/gkr636)

Garstka, M. A. and Fritzsche, S. and Lenart, I. and Hein, Z. and Jankevicius, G. and Boyle, L. H. and Elliott, T. and Trowsdale, J. and Antoniou, A. N. and Zacharias, M. and et al. Tapasin dependence of major histocompatibility complex class I molecules correlates with their conformational flexibility. The FASEB Journal, Nov, 2011, 25, pp. 3989-3998. Federation of American Society for Experimental Biology (doi:10.1096/fj.11-190249)

Droescher, M. and Begitt, A. and Marg, A. and Zacharias, M. and Vinkemeier, U. Cytokine-induced Paracrystals Prolong the Activity of Signal Transducers and Activators of Transcription (STAT) and Provide a Model for the Regulation of Protein Solubility by Small Ubiquitin-like Modifier (SUMO). Journal of Biological Chemistry, May, 2011, 286, pp. 18731-18746. American Society for Biochemistry and Molecular Biology (doi:10.1074/jbc.M111.235978)

Vargiu, Attilio V. and Collu, Francesca and Schulz, Robert and Pos, Klaas M. and Zacharias, Martin and Kleinekathöfer, Ulrich and Ruggerone, Paolo, Effect of the F610A Mutation on Substrate Extrusion in the AcrB Transporter: Explanation and Rationale by Molecular Dynamics Simulations. Journal of the American Chemical Society, Jul, 2011, 133, pp. 10704-10707. American Chemical Society (doi:10.1021/ja202666x)

Leis, Simon and Zacharias, Martin, Efficient inclusion of receptor flexibility in grid-based protein-ligand docking. Journal of Computational Chemistry, Dec, 2011, 32, pp. 3433-3439. Wiley Blackwell (John Wiley & Sons) (doi:10.1002/jcc.21923)

Braun, N. and Zacharias, M. and Peschek, J. and Kastenmuller, A. and Zou, J. and Hanzlik, M. and Haslbeck, M. and Rappsilber, J. and Buchner, J. and Weinkauf, S. Multiple molecular architectures of the eye lens chaperone αB-crystallin elucidated by a triple hybrid approach
Proceedings of the National Academy of Sciences, Dec, 2011, 108, pp. 20491-20496. Proceedings of the National Academy of Sciences (doi:10.1073/pnas.1111014108)

2010

Saladin, A. and Amourda, C. and Poulain, P. and Ferey, N. and Baaden, M. and Zacharias, M. and Delalande, O. and Prevost, C. Modeling the early stage of {DNA} sequence recognition within RecA nucleoprotein filaments. Nucleic Acids Research, Oct, 2010, 38, pp. 6313-6323. Oxford University Press (doi:10.1093/nar/gkq459)

Kannan, Srinivasaraghavan and Zacharias, Martin, Application of biasing-potential replica-exchange simulations for loop modeling and refinement of proteins in explicit solvent. Proteins: Structure, Function, and Bioinformatics, Oct, 2010, 78, pp. 2809-2819. Wiley Blackwell (John Wiley & Sons) (doi:10.1002/prot.22796)

Leis, Simon and Schneider, Sebastian and Zacharias, Martin, In Silico Prediction of Binding Sites on Proteins. Current Medicinal Chemistry, May, 2010, 17, pp. 1550-1562. Bentham Science (doi:10.2174/092986710790979944)

Fiorucci, Sébastien and Zacharias, Martin, Prediction of protein-protein interaction sites using electrostatic desolvation profiles. Biophys J, May, 2010, 98, pp. 1921--1930. (doi:10.1016/j.bpj.2009.12.4332)

Lee, Wook and Vojcic, Ljubica and Despotovic, Dragana and Prodanovic, Radivoje and Maurer, Karl-Heinz and Schwaneberg, Ulrich and Zacharias, Martin, Rationalizing perhydrolase activity of aryl-esterase and subtilisin Carlsberg mutants by molecular dynamics simulations of the second tetrahedral intermediate state. Theoretical Chemistry Accounts, Mar, 2010, 125, pp. 375-386. Springer-Verlag (doi:10.1007/s00214-009-0611-3)

El-Barghouthi, Musa I. and Saleh, Abdullah I. and Ghandour, Ahmad and Ghanem, Raed and Zacharias, Martin, Examining the potency of suggested inhibitors for the phosphatase activity of the human soluble epoxide hydrolase by molecular dynamics simulations. Journal of Molecular Structure: THEOCHEM, Mar, 2010, 944, pp. 97-104. Elsevier (doi:10.1016/j.theochem.2009.12.030)

Liang, Shide and Zheng, Dandan and Standley, Daron M and Yao, Bo and Zacharias, Martin and Zhang, Chi, EPSVR and EPMeta: prediction of antigenic epitopes using support vector regression and multiple server results. BMC Bioinformatics, 2010, 11, pp. 381. Springer (Biomed Central Ltd.) (doi:10.1186/1471-2105-11-381)

Zoda, Mohammad Safa and Zacharias, Martin and Reissmann, Siegmund, Syntheses and activities of backbone-side chain cyclic octapeptide ligands with N-functionalized phosphotyrosine for the N-terminal SH2-domain of the protein tyrosine phosphatase SHP-1.Journal of Peptide Science, Jun, 2010. Wiley Blackwell (John Wiley & Sons) (doi:10.1002/psc.1256)

Teichmann, Kathleen and Niksch, Tobias and Wieligmann, Karin and Zacharias, Martin and Imhof, Diana, Synthetic Strategies to a Backbone-Side Chain Cyclic SHP-1 N-SH2 Ligand Containing N-Functionalized Alkyl Phosphotyrosine. 
Protein \& Peptide Letters, Jul, 2010, 17, pp. 809-816. Bentham Science (doi:10.2174/092986610791306779)

Setny, Piotr and Zacharias, Martin, Hydration in Discrete Water. A Mean Field, Cellular Automata Based Approach to Calculating Hydration Free Energies. The Journal of Physical Chemistry B, Jul, 2010, 114, pp. 8667-8675. American Chemical Society (doi:10.1021/jp102462s)

Yaneva, Rakina and Schneeweiss, Clemens and Zacharias, Martin and Springer, Sebastian, Peptide binding to MHC class I and II proteins: New avenues from new methodsolecular Immunology, Jan, 2010, 47, pp. 649-657. Elsevier (doi:10.1016/j.molimm.2009.10.008)

Teichmann, Kathleen and Kühl, Toni and Könnig, Ina and Wieligmann, Karin and Zacharias, Martin and Imhof, Diana, Modulation of SHP-1 phosphatase activity by monovalent and bivalent SH2 phosphopeptide ligands. Biopolymers, Jan, 2010, 93, pp. 102-112. Wiley Blackwell (John Wiley & Sons) (doi:10.1002/bip.21307)

Fiorucci, Sebastien and Zacharias, Martin, Binding site prediction and improved scoring during flexible protein-protein docking with ATTRACT. Proteins: Structure, Function, and Bioinformatics, 2010, 78, pp. 3131--3139. Wiley Subscription Services, Inc., A Wiley Company (doi:10.1002/prot.22808)

Mueller, Berit and Zacharias, Martin and Rezwan, Kurosch, Bovine Serum Albumin and Lysozyme Adsorption on Calcium Phosphate Particles. Advanced Engineering Materials, Feb, 2010, 12, pp. B53-B61. Wiley Blackwell (John Wiley & Sons) (doi:10.1002/adem.200980024)

Zacharias, Martin, Accounting for conformational changes during protein-protein docking
Current Opinion in Structural Biology, Apr, 2010, 20, pp. 180-186. Elsevier (doi:10.1016/j.sbi.2010.02.001)

Beier, Christian and Zacharias, Martin
Tackling the challenges posed by target flexibility in drug design
Expert Opinion on Drug Discovery, Apr, 2010, 5, pp. 347-359. Informa UK (Ashley Publications) (doi:10.1517/17460441003713462)

2009

Saladin, Adrien and Fiorucci, Sebastien and Poulain, Pierre and Prevost, Chantal and Zacharias, Martin
PTools: an opensource molecular docking library
BMC Structural Biology, 2009, 9, pp. 27. (doi:10.1186/1472-6807-9-27)

Curuksu, Jeremy and Sponer, Jiri and Zacharias, Martin
Elbow Flexibility of the kt38 RNA Kink-Turn Motif Investigated by Free-Energy Molecular Dynamics Simulations
Biophysical Journal, Oct, 2009, 97, pp. 2004-2013. Elsevier (doi:10.1016/j.bpj.2009.07.031)

Kannan, Srinivasaraghavan and Zacharias, Martin
Folding of Trp-cage Mini Protein Using Temperature and Biasing Potential Replica-Exchange Molecular Dynamics Simulations
International Journal of Molecular Sciences, Mar, 2009, 10, pp. 1121-1137. MDPI AG (doi:10.3390/ijms10031121)

Liang, Shide and Zheng, Dandan and Zhang, Chi and Zacharias, Martin
Prediction of antigenic epitopes on protein surfaces by consensus scoring
BMC Bioinformatics, 2009, 10, pp. 302. Springer (Biomed Central Ltd.) (doi:10.1186/1471-2105-10-302)

Kannan, Srinivasaraghavan and Zacharias, Martin
Simulation of {DNA} double-strand dissociation and formation during replica-exchange molecular dynamics simulations
Physical Chemistry Chemical Physics, 2009, 11, pp. 10589. The Royal Society of Chemistry (doi:10.1039/b910792b)

Sieker, Florian and May, And reas and Zacharias, Martin
Predicting Affinity and Specificity of Antigenic Peptide Binding to Major Histocompatibility Class I Molecules
Current Protein \& Peptide Science, Jun, 2009, 10, pp. 286-296. Bentham Science (doi:10.2174/138920309788452191)

Kannan, Srinivasaraghavan and Zacharias, Martin
Simulated annealing coupled replica exchange molecular dynamics: An efficient conformational sampling method
Journal of Structural Biology, Jun, 2009, 166, pp. 288-294. Elsevier (doi:10.1016/j.jsb.2009.02.015)

Curuksu, J. and Zacharias, M. and Lavery, R. and Zakrzewska, K.
Local and global effects of strong {DNA} bending induced during molecular dynamics simulations
Nucleic Acids Research, Jun, 2009, 37, pp. 3766-3773. Oxford University Press (doi:10.1093/nar/gkp234)

Yaneva, Rakina and Springer, Sebastian and Zacharias, Martin
Flexibility of the MHC class II peptide binding cleft in the bound, partially filled, and empty states: A molecular dynamics simulation study
Biopolymers, Jan, 2009, 91, pp. 14-27. Wiley Blackwell (John Wiley & Sons) (doi:10.1002/bip.21078)

Frickenhaus, Stephan and Kannan, Srinivasaraghavan and Zacharias, Martin
Efficient evaluation of sampling quality of molecular dynamics simulations by clustering of dihedral torsion angles and Sammon mapping
Journal of Computational Chemistry, Feb, 2009, 30, pp. 479-492. Wiley Blackwell (John Wiley & Sons) (doi:10.1002/jcc.21076)

Bahadur, Ranjit P. and Kannan, Srinivasaraghavan and Zacharias, Martin
Binding of the Bacteriophage P22 N-Peptide to the boxB RNA Motif Studied by Molecular Dynamics Simulations
Biophysical Journal, Dec, 2009, 97, pp. 3139-3149. Elsevier (doi:10.1016/j.bpj.2009.09.035)

Curuksu, Jeremy and Zacharias, Martin
Enhanced conformational sampling of nucleic acids by a new Hamiltonian replica exchange molecular dynamics approach
The Journal of Chemical Physics, 2009, 130, pp. 104110. American Institute of Physics (doi:10.1063/1.3086832)

Kannan, Srinivasaraghavan and Zacharias, Martin
Folding simulations of Trp-cage mini protein in explicit solvent using biasing potential replica-exchange molecular dynamics simulations
Proteins: Structure, Function, and Bioinformatics, Aug, 2009, 76, pp. 448-460. Wiley Blackwell (John Wiley & Sons) (doi:10.1002/prot.22359)

2008

Zacharias, Martin
Combining Elastic Network Analysis and Molecular Dynamics Simulations by Hamiltonian Replica Exchange
Journal of Chemical Theory and Computation, Mar, 2008, 4, pp. 477-487. American Chemical Society (doi:10.1021/ct7002258)

Holzle, A. and Fischer, S. and Heyer, R. and Schutz, S. and Zacharias, M. and Walther, P. and Allers, T. and Marchfelder, A.
Maturation of the 5S rRNA 5' end is catalyzed in vitro by the endonuclease tRNase Z in the archaeon H. volcanii
RNA, Mar, 2008, 14, pp. 928-937. Cold Spring Harbor Laboratory Press (doi:10.1261/rna.933208)

Niemann, M. and Brecht, M. and Schluter, E. and Weitzel, K. and Zacharias, M. and Goringer, H. U.
TbMP42 is a structure-sensitive ribonuclease that likely follows a metal ion catalysis mechanism
Nucleic Acids Research, Jun, 2008, 36, pp. 4465-4473. Oxford University Press (doi:10.1093/nar/gkn410)

May, And reas and Zacharias, Martin
Protein-Ligand Docking Accounting for Receptor Side Chain and Global Flexibility in Normal Modes: Evaluation on Kinase Inhibitor Cross Docking
Journal of Medicinal Chemistry, Jun, 2008, 51, pp. 3499-3506. American Chemical Society (doi:10.1021/jm800071v)

May, And reas and Sieker, Florian and Zacharias, Martin
How to Efficiently Include Receptor Flexibility During Computational Docking
Current Computer Aided-Drug Design, Jun, 2008, 4, pp. 143-153. Bentham Science (doi:10.2174/157340908784533265)

May, And reas and Zacharias, Martin
Energy minimization in low-frequency normal modes to efficiently allow for global flexibility during systematic protein-protein docking
Proteins: Structure, Function, and Bioinformatics, Feb, 2008, 70, pp. 794-809. Wiley Blackwell (John Wiley & Sons) (doi:10.1002/prot.21579)

Curuksu, J. and Zakrzewska, K. and Zacharias, M.
Magnitude and direction of {DNA} bending induced by screw-axis orientation: influence of sequence, mismatches and abasic sites
Nucleic Acids Research, Feb, 2008, 36, pp. 2268-2283. Oxford University Press (doi:10.1093/nar/gkm1135)

Bahadur, R. P. and Zacharias, M. and Janin, J.
Dissecting protein-RNA recognition sites
Nucleic Acids Research, Feb, 2008, 36, pp. 2705-2716. Oxford University Press (doi:10.1093/nar/gkn102)

Sieker, Florian and Straatsma, Tjerk P. and Springer, Sebastian and Zacharias, Martin
Differential tapasin dependence of MHC class I molecules correlates with conformational changes upon peptide dissociation: A molecular dynamics simulation study
Molecular Immunology, Aug, 2008, 45, pp. 3714-3722. Elsevier (doi:10.1016/j.molimm.2008.06.009)

Bahadur, R. P. and Zacharias, M.
The interface of protein-protein complexes: Analysis of contacts and prediction of interactions
Cellular and Molecular Life Sciences, Apr, 2008, 65, pp. 1059-1072. Springer-Verlag (doi:10.1007/s00018-007-7451-x)

2007

Kannan, Srinivasaraghavan and Zacharias, Martin
Folding of a {DNA} Hairpin Loop Structure in Explicit Solvent Using Replica-Exchange Molecular Dynamics Simulations
Biophysical Journal, Nov, 2007, 93, pp. 3218-3228. Elsevier (doi:10.1529/biophysj.107.108019)

Roccatano, Danilo and Sahoo, Harekrushna and Zacharias, Martin and Nau, Werner M.
Temperature Dependence of Looping Rates in a Short Peptide
The Journal of Physical Chemistry B, Mar, 2007, 111, pp. 2639-2646. American Chemical Society (doi:10.1021/jp066418m)

Kannan, Srinivasaraghavan and Zacharias, Martin
Enhanced sampling of peptide and protein conformations using replica exchange simulations with a peptide backbone biasing-potential
Proteins: Structure, Function, and Bioinformatics, Feb, 2007, 66, pp. 697-706. Wiley Blackwell (John Wiley & Sons) (doi:10.1002/prot.21258)

May, And reas and Zacharias, Martin
Protein-protein docking in CAPRI using ATTRACT to account for global and local flexibility
Proteins: Structure, Function, and Bioinformatics, Dec, 2007, 69, pp. 774-780. Wiley Blackwell (John Wiley & Sons) (doi:10.1002/prot.21735)

Roccatano, Danilo and Barthel, And re and Zacharias, Martin
Structural flexibility of the nucleosome core particle at atomic resolution studied by molecular dynamics simulation
Biopolymers, Apr, 2007, 85, pp. 407-421. Wiley Blackwell (John Wiley & Sons) (doi:10.1002/bip.20690)

2006

Kannan, Srinivasaraghavan and Kohlhoff, Kai and Zacharias, Martin
B-{DNA} Under Stress: Over- and Untwisting of {DNA} during Molecular Dynamics Simulations
Biophysical Journal, Oct, 2006, 91, pp. 2956-2965. Elsevier (doi:10.1529/biophysj.106.087163)

Razga, Filip and Zacharias, Martin and Reblova, Kamila and Koca, Jaroslav and Sponer, Jiri
RNA Kink-Turns as Molecular Elbows: Hydration, Cation Binding, and Large-Scale Dynamics
Structure, May, 2006, 14, pp. 825-835. Elsevier (doi:10.1016/j.str.2006.02.012)

Bastard, Karine and Prevost, Chantal and Zacharias, Martin
Accounting for loop flexibility during protein-protein docking
Proteins: Structure, Function, and Bioinformatics, Mar, 2006, 62, pp. 956-969. Wiley Blackwell (John Wiley & Sons) (doi:10.1002/prot.20770)

Sahoo, Harekrushna and Roccatano, Danilo and Zacharias, Martin and Nau, Werner M.
Distance Distributions of Short Polypeptides Recovered by Fluorescence Resonance Energy Transfer in the 10 Domain
Journal of the American Chemical Society, Jun, 2006, 128, pp. 8118-8119. American Chemical Society (doi:10.1021/ja062293n)

Wong, Tuck Seng and Roccatano, Danilo and Zacharias, Martin and Schwaneberg, Ulrich
A Statistical Analysis of Random Mutagenesis Methods Used for Directed Protein Evolution
Journal of Molecular Biology, Jan, 2006, 355, pp. 858-871. Elsevier (doi:10.1016/j.jmb.2005.10.082)

Göringer, H.U. and Homann, M. and Zacharias, M. and Adler, A.
RNA Aptamers as Potential Pharmaceuticals Against Infections with African Trypanosomes
, 2006, pp. 375-393. Springer-Verlag (doi:10.1007/3-540-27262-3_19)

Sieker, F. and Springer, S. and Zacharias, M.
Comparative molecular dynamics analysis of tapasin-dependent and -independent MHC class I alleles
Protein Science, Dec, 2006, 16, pp. 299-308. Wiley Blackwell (John Wiley & Sons) (doi:10.1110/ps.062568407)

Roccatano, Danilo and Wong, Tuck Seng and Schwaneberg, Ulrich and Zacharias, Martin
Toward understanding the inactivation mechanism of monooxygenase P450 BM-3 by organic cosolvents: A molecular dynamics simulation study
Biopolymers, Dec, 2006, 83, pp. 467-476. Wiley Blackwell (John Wiley & Sons) (doi:10.1002/bip.20577)

Heck, Tobias and Limbach, Michael and Geueke, Birgit and Zacharias, Martin and Gardiner, James and Kohler, Hans-Peter E. and Seebach, Dieter
Enzymatic Degradation of beta- and Mixed alpha, beta-Oligopeptides
Chemistry \& Biodiversity, Dec, 2006, 3, pp. 1325-1348. Wiley Blackwell (John Wiley & Sons) (doi:10.1002/cbdv.200690136)

Zacharias, Martin
Minor Groove Deformability of {DNA}: A Molecular Dynamics Free Energy Simulation Study
Biophysical Journal, Aug, 2006, 91, pp. 882-891. Elsevier (doi:10.1529/biophysj.106.083816)

Ulrich Goringer, H. and Zacharias, Martin and Engstler, Markus and Homann, Matthias and Lorger, Mihaela
Serum-Stable RNA Aptamers to an Invariant Surface Domain of Live African Trypanosomes
Combinatorial Chemistry \& High Throughput Screening, Aug, 2006, 9, pp. 491-499. Bentham Science (doi:10.2174/138620706777935324)

Hampel, Kornelia and Kaufhold, Ina and Zacharias, Martin and Böhmer, Frank D. and Imhof, Diana
Phosphopeptide Ligands of the SHP-1 N-SH2 Domain: Effects on Binding and Stimulation of Phosphatase Activity
ChemMedChem, Aug, 2006, 1, pp. 869-877. Wiley Blackwell (John Wiley & Sons) (doi:10.1002/cmdc.200600037)

Barthel, And re and Zacharias, Martin
Conformational Transitions in RNA Single Uridine and Adenosine Bulge Structures: A Molecular Dynamics Free Energy Simulation Study
Biophysical Journal, Apr, 2006, 90, pp. 2450-2462.
Elsevier (doi:10.1529/biophysj.105.076158)

2005

Zacharias, M.
Vorhersage von Protein-Protein Wechselwirkungen durch Docking-Simulationen
Bioforum, 2005, 2, pp. 38-39.
(doi:)

A. Szymoszek and M. Zacharias,
Structure Prediction of Segments with Low Target–Template Similarity in Comparative Protein Modeling Using a Reduced Protein Model,
Internet Electron. J. Mol. Des., 2005, 4, pp. 659–670. (doi:)

Roccatano, Danilo and Fioroni, Marco and Zacharias, Martin and Colombo, Giorgio
Effect of hexafluoroisopropanol alcohol on the structure of melittin: A molecular dynamics simulation study
Protein Science, Oct, 2005, 14, pp. 2582-2589. Wiley Blackwell (John Wiley & Sons) (doi:10.1110/ps.051426605)

Imhof, Diana and Wieligmann, Karin and Hampel, Kornelia and Nothmann, Doreen and Zoda, Mohammad S. and Schmidt-Arras, Dirk and Zacharias, Martin and Böhmer, Frank D. and Reissmann, Siegmund
Design and Biological Evaluation of Linear and Cyclic Phosphopeptide Ligands of the N-Terminal SH2 Domain of Protein Tyrosine Phosphatase SHP-1
Journal of Medicinal Chemistry, Mar, 2005, 48, pp. 1528-1539. American Chemical Society (doi:10.1021/jm049151t)

Ihle, Y. and Ohlenschläger, O. and Häfner, S. and Duchardt, E. and Zacharias, M. and Seitz, S. and Zell, R. and Ramachandran, R. and Görlach, M.
A novel cGUUAg tetraloop structure with a conserved yYNMGg-type backbone conformation from cloverleaf 1 of bovine enterovirus 1 RNA
Nucleic Acids Research, Mar, 2005, 33, pp. 2003-2011. Oxford University Press (doi:10.1093/nar/gki501)

May, And reas and Zacharias, Martin
Accounting for global protein deformability during protein-protein and protein-ligand docking
Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, Dec, 2005, 1754, pp. 225-231. Elsevier (doi:10.1016/j.bbapap.2005.07.045)

Zacharias, Martin
ATTRACT: Protein-protein docking in CAPRI using a reduced protein model
Proteins: Structure, Function, and Bioinformatics, Aug, 2005, 60, pp. 252-256. Wiley Blackwell (John Wiley & Sons) (doi:10.1002/prot.20566)

Roccatano, Danilo and Wong, Tuck Seng and Schwaneberg, Ulrich and Zacharias, Martin
Structural and dynamic properties of cytochrome P450 BM-3 in pure water and in a dimethylsulfoxide/water mixture
Biopolymers, Aug, 2005, 78, pp. 259-267. Wiley Blackwell (John Wiley & Sons) (doi:10.1002/bip.20290)

Riemann, R. N. and Zacharias, M.
Refinement of protein cores and protein-peptide interfaces using a potential scaling approach
Protein Engineering Design and Selection, Aug, 2005, 18, pp. 465-476. Oxford University Press (doi:10.1093/protein/gzi052)

Stix, B. and Leber, Martina and Bingemer, Peter and Gross, Christof and Rüschoff, Josef and Fändrich, Marcus and Schorderet, D. F. and Vorwerk, C. K. and Zacharias, Martin and Roessner, Albert and Röcken, Christoph
Hereditary Lattice Corneal Dystrophy Is Associated with Corneal Amyloid Deposits Enclosing C-Terminal Fragments of Keratoepithelin
Investigative Ophthalmology \& Visual Science, Apr, 2005, 46, pp. 1133-1139. Association for Research in Vision and Opthalmology (doi:10.1167/iovs.04-1319)

2004

Zacharias, M.
Influence of a fluorobenzene nucleobase analogue on the conformational flexibility of RNA studied by molecular dynamics simulations
Nucleic Acids Research, Nov, 2004, 32, pp. 6304-6311. Oxford University Press (doi:10.1093/nar/gkh971)

Monie, Tom P. and Greatorex, Jane S. and Zacharias, Martin and Lever, And rew M. L.
The Human T-Cell Lymphotropic Virus Type-I Dimerization Initiation Site Forms a Hairpin Loop, Unlike Previously Characterized Retroviral Dimerization Motifs
Biochemistry, May, 2004, 43, pp. 6085-6090. American Chemical Society (doi:10.1021/bi030237i)

Gessner, G. and Zacharias, M. and Bechstedt, S. and Schönherr, R. and Heinemann, S.H.
Molecular Determinants for High-Affinity Block of Human EAG Potassium Channels by Antiarrhythmic Agents
Molecular Pharmacology, May, 2004, 65, pp. 1120-1129. American Society for Pharmacology & Experimental Therapeutics (doi:10.1124/mol.65.5.1120)

Zacharias, Martin
Rapid protein-ligand docking using soft modes from molecular dynamics simulations to account for protein deformability: Binding of FK506 to FKBP
Proteins: Structure, Function, and Bioinformatics, Mar, 2004, 54, pp. 759-767. Wiley Blackwell (John Wiley & Sons) (doi:10.1002/prot.10637)

Wright, Cynthia Anne and Kozik, Patrycja and Zacharias, Martin and Springer, Sebastian
Tapasin and other chaperones: models of the MHC class I loading complex
Biological Chemistry, Jan, 2004, 385. Walter de Gruyter GmbH (doi:10.1515/BC.2004.100)

Frank, C. and Burkhardt, C. and Imhof, D. and Ringel, J. and Zschörnig, O. and Wieligmann, K. and Zacharias, M. and Böhmer, F.D.
Effective Dephosphorylation of Src Substrates by SHP-1
Journal of Biological Chemistry, Jan, 2004, 279, pp. 11375-11383. American Society for Biochemistry and Molecular Biology (doi:10.1074/jbc.M309096200)

Villescas-Diaz, Gilberto and Zacharias, Martin
Efficient Search on Energy Minima for Structure Prediction of Nucleic Acid Motifs
Journal of Biomolecular Structure and Dynamics, Dec, 2004, 22, pp. 355-364. Informa UK (Taylor & Francis) (doi:10.1080/07391102.2004.10507007)

Roccatano, D. and Nau, W. M. and Zacharias, M.
Structural and Dynamic Properties of the CAGQW Peptide in Water: A Molecular Dynamics Simulation Study Using Different Force Fields
The Journal of Physical Chemistry B, Dec, 2004, 108, pp. 18734-18742. American Chemical Society (doi:10.1021/jp0475077)

Riemann, R.N. and Zacharias, M.
Reversible scaling of dihedral angle barriers during molecular dynamics to improve structure prediction of cyclic peptides
Journal of Peptide Research, Apr, 2004, 63, pp. 354-364. Wiley Blackwell (Blackwell Publishing) (doi:10.1111/j.1399-3011.2004.00110.x)

2003

Zacharias, M.
Perspectives of Drug Design that Targets RNA
Current Medicinal Chemistry -Anti-Infective Agents, Jun, 2003, 2, pp. 161-172. Bentham Science (doi:10.2174/1568012033483088)

Zacharias, Martin
Protein-protein docking with a reduced protein model accounting for side-chain flexibility
Protein Science, Jun, 2003, 12, pp. 1271-1282. Wiley Blackwell (John Wiley & Sons) (doi:10.1110/ps.0239303)

Villescas-Diaz, Gilberto and Zacharias, Martin
Sequence Context Dependence of Tandem Guanine:Adenine Mismatch Conformations in RNA: A Continuum Solvent Analysis
Biophysical Journal, Jul, 2003, 85, pp. 416-425. Elsevier (doi:10.1016/S0006-3495(03)74486-5)

Zacharias, Martin
Continuum Solvent Modeling of Nonpolar Solvation: Improvement by Separating Surface Area Dependent Cavity and Dispersion Contributions
The Journal of Physical Chemistry A, Apr, 2003, 107, pp. 3000-3004. American Chemical Society (doi:10.1021/jp027598c)

2002

Wieligmann, Karin and Castro, Luis Felipe Pineda De and Zacharias, Martin
Molecular Dynamics Simulations on the Free and Complexed N-Terminal SH2 Domain of SHP-2
In Silico Biology, 2002, 2, pp. 305-311. (doi:)

De Castro, L. F. Pineda and Zacharias, M.
DAPI binding to the {DNA} minor groove: a continuum solvent analysis
Journal of Molecular Recognition, Jul, 2002, 15, pp. 209-220. Wiley Blackwell (John Wiley & Sons) (doi:10.1002/jmr.581)

2001

Burkhardt, C. and Zacharias, M.
Modelling ion binding to AA platform motifs in RNA: a continuum solvent study including conformational adaptation.
Nucleic Acids Res, Oct, 2001, 29, pp. 3910--3918. (doi:10.1093/nar/29.19.3910)

Zacharias, Martin
Conformational Analysis of {DNA}-Trinucleotide-Hairpin-Loop Structures Using a Continuum Solvent Model
Biophysical Journal, May, 2001, 80, pp. 2350-2363. Elsevier (doi:10.1016/S0006-3495(01)76205-4)

Feig, Michael and Zacharias, Martin and Pettitt, B. Montgomery
Conformations of an Adenine Bulge in a {DNA} Octamer and Its Influence on {DNA} Structure from Molecular Dynamics Simulations
Biophysical Journal, Jul, 2001, 81, pp. 352-370. Elsevier (doi:10.1016/S0006-3495(01)75705-0)

2000

Zacharias, M. and Sklenar, H.
Conformational Deformability of RNA: A Harmonic Mode Analysis
Biophysical Journal, May, 2000, 78, pp. 2528-2542. Elsevier (doi:10.1016/S0006-3495(00)76798-1)
 
Zacharias, Martin
Simulation of the structure and dynamics of nonhelical RNA motifs
Current Opinion in Structural Biology, Jun, 2000, 10, pp. 311-317. Elsevier (doi:10.1016/S0959-440X(00)00089-0)
 
Zacharias, Martin
Comparison of molecular dynamics and harmonic mode calculations on RNA
Biopolymers, Dec, 2000, 54, pp. 547-560. Wiley Blackwell (John Wiley & Sons) (doi:10.1002/1097-0282(200012)54:7<547::AID-BIP70>3.0.CO;2-N)

1999

Zacharias, Martin and Sklenar, Heinz
Conformational analysis of single-base bulges in A-form {DNA} and RNA using a hierarchical approach and energetic evaluation with a continuum solvent model
Journal of Molecular Biology, Jun, 1999, 289, pp. 261-275. Elsevier - Academic Press (doi:10.1006/jmbi.1999.2760)
 
Zacharias, Martin and Sklenar, Heinz
Harmonic modes as variables to approximately account for receptor flexibility in ligand-receptor docking simulations: Application to {DNA} minor groove ligand complex
Journal of Computational Chemistry, Feb, 1999, 20, pp. 287-300. Wiley Blackwell (John Wiley & Sons) (doi:10.1002/(SICI)1096-987X(199902)20:3<287::AID-JCC1>3.0.CO;2-H)

1997

Zacharias, M. and Hagerman, P.J.
Influence of static and dynamic bends on the birefringence decay profile of RNA helices: Brownian dynamics simulations
Biophysical Journal, Jul, 1997, 73, pp. 318-332. Elsevier (doi:10.1016/S0006-3495(97)78072-X)
 
Zacharias, M. and Sklenar, H.
Analysis of the stability of looped-out and stacked-in conformations of an adenine bulge in {DNA} using a continuum model for solvent and ions
Biophysical Journal, Dec, 1997, 73, pp. 2990-3003. Elsevier (doi:10.1016/S0006-3495(97)78328-0)

1996

Zacharias, Martin and Hagerman, Paul J.
The Influence of Symmetric Internal Loops on the Flexibility of RNA
Journal of Molecular Biology, Mar, 1996, 257, pp. 276-289. Elsevier - Academic Press (doi:10.1006/jmbi.1996.0162)

1995

Zacharias, Martin and Hagerman, Paul J.
Bulge-Induced Bends in RNA: Quantification by Transient Electric Birefringence
Journal of Molecular Biology, Mar, 1995, 247, pp. 486-500. Elsevier - Academic Press (doi:10.1006/jmbi.1995.0155)

Zacharias, M. and Straatsma, T. P.
Path Dependence of Free Energy Components in Thermodynamic Integration
Molecular Simulation, Jun, 1995, 14, pp. 417-423. Informa UK (Taylor & Francis) (doi:10.1080/08927029508022035)

1994

Zacharias, M. and Straatsma, T. P. and McCammon, J. A.
Separation-shifted scaling, a new scaling method for Lennard-Jones interactions in thermodynamic integration
The Journal of Chemical Physics, 1994, 100, pp. 9025. American Institute of Physics (doi:10.1063/1.466707)

Zacharias, M. and Luty, B.A. and Davis, M.E. and McCammon, J.A.
Combined Conformational Search and Finite-Difference Poisson-Boltzmann Approach for Flexible Docking
Journal of Molecular Biology, May, 1994, 238, pp. 455-465. Elsevier - Academic Press (doi:10.1006/jmbi.1994.1304)

1993

Wagner, Rolf and Theißen, Günter and Zacharias, Martin
Regulation of Ribosomal RNA Synthesis and Control of Ribosome Formation in E. Coli
, 1993, pp. 119-130. Springer US (doi:10.1007/978-1-4615-2407-6_12)

Straatsma, T.P. and Zacharias, M. and McCammon, J.A.
Free energy difference calculations in biomolecular systems
Computer Simulation of Biomolecular Systems, 1993, 2, pp. 349-367. (doi:)

Zacharias, M. and Straatsma, T. P. and McCammon, J. A. and Quiocho, F. A.
Inversion of receptor binding preferences by mutagenesis: Free energy thermodynamic integration studies on sugar binding to L-arabinose binding proteins
Biochemistry, Jul, 1993, 32, pp. 7428-7434. American Chemical Society (doi:10.1021/bi00080a013)

1992

Straatsma, T.P. and Zacharias, M. and McCammon, J.A.
Holonomic constraint contributions to free energy differences from thermodynamic integration molecular dynamics simulations
Chemical Physics Letters, Aug, 1992, 196, pp. 297-302. Elsevier (doi:10.1016/0009-2614(92)85971-C)

1991
Zacharias, M. and Theissen, G. and Bradaczek, C. and Wagner, R.
Analysis of sequence elements important for the synthesis and control of ribosomal RNA in E coli
Biochimie, Jun, 1991, 73, pp. 699-712. Elsevier (doi:10.1016/0300-9084(91)90050-B)

1990

Zacharias, Martin and Wagner, Rolf and Göringer, H. Ulrich
Polyacrylamide gradient gel electrophoresis for the detection of bended {DNA} fragments
Nucleic Acids Research, 1990, 18, pp. 2827-2827. Oxford University Press (doi:10.1093/nar/18.9.2827)

Zacharias, M. and Goeringer, H.U. and Wagner, R.
The signal for growth rate control and stringent sensitivity in E. coli is not restricted to a particular sequence motif within the promoter region
Nucleic Acids Research, 1990, 18, pp. 6271-6275. Oxford University Press (doi:10.1093/nar/18.21.6271)

TheiBen, Günter and Eberie, Jürgen and Zacharias, Martin and Tobias, Luise and Wagner, Rolf
The tL structure within the leader region of Escherichia coli ribosomal RNA operons has post-transcriptional functions
Nucleic Acids Research, 1990, 18, pp. 3893-3901. (doi:10.1093/nar/18.13.3893)

1989

M. Zacharias and H. Ulrich Göringer and R. Wagner
Influence of the GCGC discriminator motif introduced into the ribosomal RNA P2- and tac promoter on growth-rate control and stringent sensitivity.
The EMBO journal, 1989, 8, pp. 3357--63. (doi:)

Zacharias, M. and Wagner, R.
Functional characterization of a putative internal promoter sequence between the 16S and the 23S RNA genes within the Escherichia coli rrnB operon.
Molecular Microbiology, Mar, 1989, 3, pp. 405-410. Wiley Blackwell (Blackwell Publishing)