Sühnel Laboratory Publications

Aumann F, Sühnel J, Langowski J, Diekmann S. (2010) Rigid assembly and Monte Carlo models of stable and unstable chromatin structures: the effect of nucleosomal spacing. Theor Chem Accounts. 125, 217-231.

Fuellen G, Adjaye J, de Grey A, Lepperdinger G, de Magalhães JP, Sühnel J, Wipat A (2010) Bioinformatics in aging research: a workshop report. Rejuvenation Res. 13, 763-767. [PubMed]

Hollunder J, Friedel M, Kuiper M, Wilhelm T. (2010) DASS-GUI: a user interface for identification and analysis of significant patterns in non-sequential data. Bioinformatics. 26, 987-989. [PubMed]

Stucken K, John U, Cembella A, Murillo AA, Soto-Liebe K, Fuentes-Valdés JJ, Friedel M, Plominsky AM, Vásquez M, Glöckner G. (2010) The smallest known genomes of multicellular and toxic cyanobacteria: comparison, minimal gene sets for linked traits and the evolutionary implications. PLoS One. 5, e9235. [PubMed]

Friedel M, Nikolajewa S, Sühnel J, Wilhelm T. (2009) DiProGB: The Dinucleotide Properties Genome Browser Bioinformatics. 25, 2603-2604. [PubMed]

Friedel M, Nikolajewa S, Sühnel J, Wilhelm T. (2009) DiProDB: a database for dinucleotide properties. Nucleic Acids Res. 37 (Database issue), D37-40. [PubMed]

Ibrahim B, Schmitt E, Dittrich P, Diekmann S. (2009) In silico study of kinetochore control, amplification, and inhibition effects in MCC assembly. Biosystems. 95, 35-50. [PubMed]

Friedel M, Nikolajewa S, Wilhelm T. (2008) The decomposition tree for analyses of boolean functions. Math Struct in Comp Science. 18, 411-426.

Ibrahim B, Diekmann S, Schmitt E, Dittrich P. (2008) In-silico modeling of the mitotic spindle assembly checkpoint. PLoS One. 3, e1555. [PubMed]

Ibrahim B, Dittrich P, Diekmann S, Schmitt E. (2008) Mad2 binding is not sufficient for complete Cdc20 sequestering in mitotic transition control (an in silico study). Biophys Chem. 134, 93-100. [PubMed]

Meyer M, Sühnel J. (2008) Density functional study of adenine tetrads with N6-H6...N3 hydrogen bonds. J Phys Chem A. 112, 4336-4341. [PubMed]

Altenberg B, Rapp A, Schmitt E, Greulich KO. (2007) Expression levels of 63 p53-related genes add up to similar values in 24 different tissues and are unified in cancer. Genomics. 90, 661-673. [PubMed]

Hühne R, Koch FT, Sühnel J. (2007) A comparative view of comprehensive information resources on three dimensional structures of biological macromolecules. Brief Funct Genomic Proteomic. 6, 220-239. [PubMed]

Ibrahim B, Dittrich P, Diekmann S, Schmitt E. (2007) Stochastic effects in a compartmental model for mitotic checkpoint regulation. J Integrative Bioinformatics. 4, 10-01.

Meyer M, Steinke T, Sühnel J. (2007) Density functional study of isoguanine tetrad and pentad sandwich complexes with alkali metal ions. J Mol Model. 13, 335-345. [PubMed]

Romualdi A, Felder M, Rose D, Gausmann U, Schilhabel M, Glöckner G, Platzer M, Sühnel J. (2007) GenColors: annotation and comparative genomics of prokaryotes made easy. Methods Mol Biol. 395, 75-96. [PubMed]

Schwarz-Finsterle J, Stein S, Grossmann C, Schmitt E, Trakhtenbrot L, Rechavi G, Amariglio N, Cremer C, Hausmann M. (2007) Comparison of triple helical COMBO-FISH and standard FISH by means of quantitative microscopic image analysis of abl/bcr positions in cell nuclei. J Biochem Biophys Methods. 70, 397-406. [PubMed]

Skerka C, Lauer N, Weinberger AA, Keilhauer CN, Sühnel J, Smith R, Schlötzer-Schrehardt U, Fritsche L, Heinen S, Hartmann A, Weber BH, Zipfel PF. (2007) Defective complement control of factor H (Y402H) and FHL-1 in age-related macular degeneration. Mol Immunol. 44, 3398-3406. [PubMed]

Behrens S, Habicht W, Wagner K, Unger E. (2006) Assembly of nanoparticle ring structures based on protein templates. Adv Mat. 18, 284-289.

Glöckner G, Schulte-Spechtel U, Schilhabel M, Felder M, Sühnel J, Wilske B, Platzer M. (2006) Comparative genome analysis: selection pressure on the Borrelia vls cassettes is essential for infectivity. BMC Genomics. 7, 211. [PubMed]

Gutermann A, Mayer E, von Dehn-Rothfelser K, Breidenstein C, Weber M, Muench M, Gungor D, Suehnel J, Moebius U, Lechmann M. (2006) Efficacy of oncolytic herpesvirus NV1020 can be enhanced by combination with chemotherapeutics in colon carcinoma cells. Hum Gene Ther. 17, 1241-1253. [PubMed]

Nolte O, Müller M, Häfner B, Knemeyer JP, Stöhr K, Wolfrum J, Hakenbeck R, Denapaite D, Schwarz-Finsterle J, Stein S, Schmitt E, Cremer C, Herten DP, Hausmann M, Sauer M. (2006) Novel singly labelled probes for life science applications (SMART PROBES). In: Biophotonics: Visions for Better Health Care (Eds. Popp J, Strehle M), Wiley-VCH, 167-230.

Hausmann M, Hildenbrand G, Schwarz-Finsterle J, Spöri U, Schneider H, Schmitt E, Cremer C. (2005) New technologies measure genome domains - High resolution microscopy and novel labeling procedures enable 3-D studies of the functional architecture of gene domains in cell nuclei. Biophotonics Int. 12, 34-37.

Imhof D, Wieligmann K, Hampel K, Nothmann D, Zoda MS, Schmidt-Arras D, Zacharias M, Böhmer FD, Reissmann S. (2005) Design and biological evaluation of linear and cyclic phosphopeptide ligands of the N-terminal SH2 domain of protein tyrosine phosphatase SHP-1. J Med Chem. 48, 1528-1539. [PubMed]

Meyer M, Hocquet A, Sühnel J. (2005) Interaction of sodium and potassium ions with sandwiched cytosine-, guanine-, thymine-, and uracil-base tetrads. J Comput Chem. 26, 352-364. [PubMed]

Monajembashi S, Rapp A, Schmitt E, Dittmar H, Greulich KO, Hausmann M. (2005) Spatial association of homologous pericentric regions in human lymphocyte nuclei during repair. Biophys J. 88, 2309-2322. [PubMed]

Riemann RN, Zacharias M. (2005) Refinement of protein cores and protein-peptide interfaces using a potential scaling approach. Protein Eng Des Sel. 18, 465-476. [PubMed]

Romualdi A, Siddiqui R, Glöckner G, Lehmann R, Sühnel J. (2005) GenColors: accelerated comparative analysis and annotation of prokaryotic genomes at various stages of completeness. Bioinformatics. 21, 3669-3671. [PubMed]

Schwarz-Finsterle J, Stein S, Grossmann C, Schmitt E, Schneider H, Trakhtenbrot L, Rechavi G, Amariglio N, Cremer C, Hausmann M. (2005) COMBO-FISH for focussed fluorescence labelling of gene domains: 3D-analysis of the genome architecture of abl and bcr in human blood cells. Cell Biol Int. 29, 1038-1046. [PubMed]

Wieland GD, Nehmann N, Müller D, Eibel H, Siebenlist U, Sühnel J, Zipfel PF, Skerka C. (2005) Early growth response proteins EGR-4 and EGR-3 interact with immune inflammatory mediators NF-κB p50 and p65. J Cell Sci. 118, 3203-3212. [PubMed]

Frank C, Burkhardt C, Imhof D, Ringel J, Zschörnig O, Wieligmann K, Zacharias M, Böhmer FD. (2004) Effective dephosphorylation of Src substrates by SHP-1. J Biol Chem. 279, 11375-11383. [PubMed]

Glöckner G, Lehmann R, Romualdi A, Pradella S, Schulte-Spechtel U, Schilhabel M, Wilske B, Sühnel J, Platzer M. (2004) Comparative analysis of the Borrelia garinii genome. Nucleic Acids Res. 32, 6038-6046. [PubMed]

Groten JP, Cassee FR, van Bladeren PJ, de Rosa C, Feron VJ, Sühnel J. (2004) Mischungen chemischer Stoffe. In: Lehrbuch der Toxikologie, (Hrsg. Marquardt H, Schäfer SG), ISBN: 3804717772, Wissenschaftliche Verlagsgesellschaft, Stuttgart, Kap. 13, pp. 287-302. [Amazon]

Riemann NM, Zacharias M. (2004) Reversible scaling of dihedral angle barriers during molecular dynamics to improve structure prediction of cyclic peptides. J Pept Res. 63, 354-364. [PubMed]

Schönecker B, Zheldakova T, Lange C, Günther W, Görls H, Bohl M. (2004) Intramolecular gamma-hydroxylations of nonactivated C-H bonds with copper complexes and molecular oxygen. Chemistry. 10, 6029-6042. [PubMed]

Szymoszek A, Zacharias M. (2004) Reduced protein model as a tool in the homology modeling. Internet Electron J Mol Des, November 29 - December 12 [Journal Link]

Villescas-Diaz G, Zacharias M. (2004) Efficient search on energy minima for structure prediction of nucleic acid motifs. J Biomol Struct Dyn. 22, 355-364. [PubMed]

Hausmann M, Winkler R, Hildenbrand G, Finsterle J, Weisel A, Rapp A, Schmitt E, Janz S, Cremer C. (2003) COMBO-FISH: specific labeling of nondenatured chromatin targets by computer-selected DNA oligonucleotide probe combinations. Biotechniques. 35, 564-577. [PubMed]

Kronen M, Görls H, Nguyen HH, Reissmann S, Bohl M, Sühnel J, Gräfe U. (2003) Crystal structure and conformational analysis of ampullosporin A. J Peptide Sci. 9, 729-744. [PubMed]

Louit G, Hoquet A, Ghomi M, Meyer M, Sühnel J. (2003) Guanine tetrads interacting with metal ions. An AIM topological analysis of the electron density. Phys Chem Comm. 6, 1-5.

Meyer M, Sühnel J. (2003) Base polyad motifs in nucleic acids - Biological significance, occurrence in three-dimensional experimental structures and computational studies. In: Computational Chemistry: Reviews of Current Trends, Vol. 8, (Ed. Leszczynski J), ISBN: 981-238-702-1, World Scientific Publishing Company, Chapter 4, pp. 161-208.

Meyer M, Sühnel J. (2003) Computational studies on base tetrad motifs in nucleic acid structures - Quantum chemistry helps to understand biology. Berichte des IZWR (Friedrich-Schiller-Universität Jena), Band, 43-60. [PDF] not peer-reviewed

Meyer M, Sühnel J. (2003) Interaction of cyclic cytosine-, guanine-, thymine-, uracil- and mixed guanine-cytosine base tetrads with K+, Na+ and Li+ ions -- a density functional study. J Biomol Struct Dyn. 20, 507-517. [PubMed]

Meyer M, Sühnel J. (2003) Self-association of isoguanine nucleobases and molecular recognition of alkaline ions: Tetrad versus pentad structures. J Phys Chem A. 107, 1025-1031.

Villescas-Diaz G, Zacharias M. (2003) Sequence context dependence of tandem guanine:adenine mismatch conformations in RNA: a continuum solvent analysis. Biophys J. 85, 416-425. [PubMed]

Behrens S, Rahn K, Habicht W, Böhm KJ, Rösner H, Dinjus E, Unger E. (2002) Nanoscale particle arrays induced by highly ordered protein assemblies. Adv Mat. 14, 1621-1625.

Louit G, Hoquet A, Ghomi M, Meyer M, Sühnel J. (2002) Are guanine tetrads stabilised by bifurcated hydrogen bonds: An AIM topological analysis of electron density. Phys Chem Comm. 5, 94-98.

Pal D, Sühnel J, Weiss MS. (2002) New principles of protein structure: nests, eggs and what next? Angew Chem Int Ed Engl. 41, 4663-4665. [PubMed]

Rahn K, Sühnel J. (2002) Das Jenaer Centrum für Bioinformatik. Bioforum. 7-8, 454-455. [PDF] not peer-reviewed

Reichert J, Sühnel J. (2002) The IMB Jena Image Library of Biological Macromolecules - 2002 update. Nucleic Acids Res. 30, 253-254. [PubMed]

Sühnel J. (2002) Beyond nucleic acid base pairs: from triads to heptads. Biopolymers. 61, 32-51. [PubMed]

Brandl M, Meyer M, Sühnel J. (2001) Quantum-chemical analysis of C-H...O and C-H...N interactions in RNA base pairs--H-bond versus anti-H-bond pattern. J Biomol Struct Dyn. 18, 545-555. [PubMed]

Brandl M, Weiss MS, Jabs A, Sühnel J, Hilgenfeld R. (2001) C-H...pi-interactions in proteins. J Mol Biol. 307, 357-377. [PubMed]

Groten JP, Feron VJ, Sühnel J. (2001) Toxicology of simple and complex mixtures. Trends Pharmacol Sci. 22, 316-322. [PubMed]

Meyer M, Brandl M, Sühnel J. (2001) Are guanine tetrads stabilized by bifurcated hydrogen bonds? J Phys Chem A. 105, 8223-8225.

Meyer M, Schneider C, Brandl M, Sühnel J. (2001) Cyclic adenine-, cytosine-, thymine- and mixed guanine-cytosine- base tetrads in nucleic acids viewed from a quantum-chemical and force field perspective. J Phys Chem A. 105, 11560-11573.

Meyer M, Steinke T, Brandl M, Sühnel J. (2001) Density functional study of guanine and uracil quartets and of guanine/metal ion complexes. J Comp Chem. 22, 109-124.

Schneider C, Brandl M, Sühnel J. (2001) Molecular dynamics simulation reveals conformational switching of water-mediated uracil-cytosine base-pairs in an RNA duplex. J Mol Biol. 305, 659-667. [PubMed]

Weiss MS, Brandl M, Sühnel J, Pal D, Hilgenfeld R. (2001) More hydrogen bonds for the (structural) biologist. Trends Biochem Sci. 26, 521-523. [PubMed]

Brandl M, Meyer M, Sühnel J. (2000) Water-mediated base pairs in RNA - a quantum-chemical study. J Phys Chem A. 104, 11177-11187.

Reichert J, Jabs A, Slickers P, Sühnel J. (2000) The IMB Jena Image Library of biological macromolecules. Nucleic Acids Res. 28, 246-249. [PubMed I Supplementary Material]

Schneider C, Sühnel J. (2000) A molecular dynamics simulation study of coaxial stacking in RNA. J Biomol Struct Dyn. 18, 345-352. [PubMed]

Brandl M, Lindauer K, Meyer M, Sühnel J. (1999) C-H...O and C-H...N interactions in RNA structures. Theor Chem Acc. 101, 103-113. (Special Issue of the European Conference 'Computational Chemistry and the Living World: From Sequence to Function', Chambery / France, April 20-24, 1998)

Brandl M, Meyer M, Sühnel J. (1999) Quantum-chemical study of a water-mediated uracil-cytosine base pair. J Amer Chem Soc. 121, 2605-2606.

Cassee FR, Sühnel J, Groten JP, Feron V. (1999) Toxicology of chemical mixtures. In: General and Applied Toxicology (Eds. Ballantyne B, Marrs TC, Syverson T), MacMillan Reference Ltd., Oxford, 2nd Ed., Vol. 1, ch. 14, pp. 303-319.

Dressler V, Müller G, Sühnel J. (1999) CombiTool - a new computer program for analyzing combination experiments with biologically active agents. Comput Biomed Res. 32, 145-160. [PubMed]

Schneider C, Sühnel J. (1999) A molecular dynamics simulation of the flavin mononucleotide-RNA aptamer complex. Biopolymers. 50, 287-302. [PubMed]

Sühnel J. (1999) Computer modeling of protein, nucleic acid, and drug structures. In: Microsystem Technology: A Powerful Tool for Biomolecular Studies (Eds. Saluz HP, Köhler M), Birkhäuser Verlag, Basel, 475-505.

Meyer M, Schomburg D. (1998) Protein interactions. In: Biotechnology (Eds. Rehm HJ, Reed G), Vol. 5, Recombinant Proteins, Monoclonal Antibodies and Therapeutic Genes, VCH, Weinheim, 48-68.

Meyer M, Wohlfahrt G, Knäblein J, Schomburg D. (1998) Aspects of the mechanism of catalysis of glucose oxidase: a docking, molecular mechanics and quantum chemical study. J Comput Aided Mol Des. 12, 425-440. [PubMed]

Reichert J, Jabs A, Sühnel J. (1998) Virtual reality modeling. Nachrichten aus Chemie, Technik und Laboratorium. 46, A64-A68. [preprint version in PDF format]

Slickers P, Hillebrand M, Kittler L, Löber G, Sühnel J. (1998) Molecular modelling and footprinting studies of DNA minor groove binders: bisquaternary ammonium heterocyclic compounds. Anticancer Drug Des. 13, 463-488. [PubMed]

Sühnel J. (1998) Parallel dose-response curves in combination experiments. Bull Math Biol. 60, 197-213. [PubMed]

Cassidy SA, Slickers P, Trent JO, Capaldi DC, Roselt PD, Reese CB, Neidle S, Fox KR. (1997) Recognition of GC base pairs by triplex forming oligonucleotides containing nucleosides derived from 2-aminopyridine. Nucleic Acids Res. 25, 4891-4898. [PubMed]

Meyer M, Sühnel J. (1997) Quantum-chemical ab initio study on the adenine-difluorotoluene complex--a mimic for the adenine-thymine base pair. J Biomol Struct Dyn. 15, 619-624. [PubMed]

Sühnel J. (1997) Views of RNA on the World Wide Web. Trends Genet. 13, 206-207. [PubMed]

Sühnel J. (1997) Virtual reality modeling for structural biology. In: Proceedings of the German Conference on Bioinformatics - GCB '96 (Eds. Hofestädt R, Lengauer T, Löffler M, Schomburg D), Lecture notes in computer science, Vol. 1278, Springer-Verlag Berlin, 189-198. [Book Link]

Sühnel J, Hermann G, Dornberger U, Fritzsche H. (1997) Computer analysis of phytochrome sequences and reevaluation of the phytochrome secondary structure by Fourier transform infrared spectroscopy. Biochim Biophys Acta. 1340, 253-267. [PubMed]

Vogt T, Zimmermann E, Grimm R, Meyer M, Strack D. (1997) Are the characteristics of betanidin glucosyltransferases from cell-suspension cultures of Dorotheanthus bellidiformis indicative of their phylogenetic relationship with flavonoid glucosyltransferases? Planta. 203, 349-361. [PubMed]

Lindauer K, Bendic C, Sühnel J. (1996) HBexplore - a new tool for identifying and analysing hydrogen bonding patterns in biological macromolecules. Comput Appl Biosci. 12, 281-289. [PubMed]

Sühnel J. (1996) Image library of biological macromolecules. Comput Appl Biosci. 12, 227-229. [PubMed]

Sühnel J. (1996) Zero interaction response surfaces for combined-action assessment. Food Chem Toxicol. 34, 1151-1153. [PubMed]

Recknagel R-D, Weller K, Köhler JM. (1993) A simple method to forecast good promoters of Escherichia coli by means of doublet frequencies. J Theor Biol. 162, 75-80. [PubMed]

Sühnel J. (1993) Evaluation of interaction in olfactory and taste mixtures. Chemical Senses. 18, 131-149.

Sühnel, J. (1993) The Marcus cross relation for hydrogen transfer reactions. J Phys Org Chem. 6, 281-286.

Greco WR, Unkelbach HD, Pöch G, Sühnel J, Kundi M, Bödeker W. (1992) Consensus on concepts and terminology for combined-action assessment: the Saariselkä agreement. Archives of Complex Environmental Studies. 4, 65-69.

Sühnel J. (1992) Assessment of the interaction of biologically active agents by means of the isobole approach: Fundamental assumptions and recent developments. Archives of Complex Environmental Studies. 4, 35-44.

Sühnel J. (1992) Comment on the paper: A three-dimensional model to analyze drug-drug interactions. Prichard, M.N. and Shipman, C., Jr. (1990) Antiviral Res. 14, 181-206. Antiviral Res. 17, 91-93. [PubMed]

Sühnel J. (1992) Re: W. R. Greco et al., Application of a new approach for the quantitation of drug synergism to the combination of cis-diamminedichloroplatinum and 1-beta-D-arabinofuranosylcytosine. Cancer Res. 52, 4560-4561. [PubMed]

Sühnel J. (1992) Zero interaction response surfaces, interaction functions and difference response surfaces for combinations of biologically active agents. Arzneimittelforschung. 42, 1251-1258. [PubMed]