K. J. Jalkanen, J. D. Gale, P. R. Lassen, L. Hemmingsen, A. Rodarte, I. M. Degtyarenko, R. M. Nieminen, S. Brøgger Christensen, M. Knapp-Mohammady and S. Suhai:
A configurational and conformational study of aframodial and its diasteriomers via experimental and theoretical VA and VCD spectroscopies,
Theor. Chem. Account 119, 177-190 (2008).
S. Tiwari, P. C. Mishra and S. Suhai:
Solvent effect of aqueous media on properties of glycine: Significance of specific and bulk solvent effects, and geometry optimization in aqueous media,
Int. J. Quant. Chem. 108, 1004-1016 (2008).
M. Knapp-Mohammady, N. H. March and S. Suhai:
Geometry and ground-state electronic structure of neutral ruthenium metal complexes of potential relevance to metal-based drugs for cancer control,
Phys Lett. A 372, 1881-1884 (2008).
A. Kumar, M. D. Sevilla and S. Suhai:
Microhydration of the guanine-cytosine (GC) base pair in the neutral and anionic radical states: A density functional study,
J. Phys. Chem. B 112, 5189-5198 (2008).
E.A. Afanasyeva, A. Hotz-Wagenblatt, K. H. Glatting and F. Westermann:
New miRNAs cloned from neuroblastoma.
BMC Genomics 9, 52 (2008).
C. Münk, T. Beck, J. Zielonka, A. Hotz-Wagenblatt, S. Chareza, M. Battenberg,
J. Thielebein, K. Cichutek, I. G. Bravo, S. J. O'Brien, M. Löchelt, N. Yuhki:
Functions, structure, and read-through alternative splicing of feline APOBEC3 genes.
Genome Biol 9, R48 (2008).
C. Tschuch, A. Schulz, A. Pscherer, W. Werft, A. Benner, A. Hotz-Wagenblatt,
L. S. Barrionuevo, P. Lichter and D. Mertens:
Off-target effects of siRNA specific for GFP.
BMC Mol Biol 9, 60 (2008).
N. H. March and S. Suhai:
Can density functional theory make use of experimentally determined ground-state electron densities via the Dirac density matrix for molecules of biological interest?
Phys. Lett. A 360, 665-668 (2007).
A.-N. Bondar, S. Suhai, S. Fischer, J. C. Smith and M. Elstner:
Suppression of the back proton-transfer from Asp85 to the retinal Schiff base in bacteriorhodopsin: A theoretical analysis of structural elements,
J. Struct. Biol. 157, 454-469 (2007).
P. K. Shukla, P. C. Mishra and S. Suhai:
Reactions of guanine with methyl chloride and methyl bromide: O6-methylation versus charge transfer complex formation,
Int. J. Quant. Chem. 107, 1270-1283 (2007).
N. C. Polfer, J. Oomens, S. Suhai and B. Paizs:
Infrared spectroscopy and theoretical studies on gas-phase protonated Leu-enkephalin and its fragments: Direct experimental evidence for the mobile proton,
J. Am. Chem. Soc. 129, 5887-5897 (2007).
C. del Val, P. Ernst, M. Falkenhahn, C. Fladerer, K. H. Glatting, S. Suhai and A. Hotz-Wagenblatt:
ProtSweep, 2Dsweep and DomainSweep: protein analysis suite at DKFZ,
Nuc. Acids Res. 35, W444-W450 (2007). [doi: 10.1093/nar/gkm364]
M. N. Blom, I. Compagnon, N. C. Polfer, G. von Helden, G. Meijer, S. Suhai, B. Paizs and J. Oomens:
Stepwise solvation of an amino acid: The appearance of zwitterionic structures,
J. Phys. Chem. A 111, 7309-7316 (2007).
F. A. Giordano, A. Hotz-Wagenblatt, D. Lauterborn, J.-U. Appelt, K. Fellenberg, K. Z. Nagy, W. J. Zeller, S. Suhai, S. Fruehauf and S. Laufs:
New bioinformatic strategies to rapidly characterize retroviral integration sites of gene therapy vectors,
Methods Inf. Med. 46, 542-547 (2007).
A.-N. Bondar, S. Suhai, J. C. Smith and P. T. Frangopol:
Computer simulations of local anesthetics mechanism: Quantum chemical investigation of procaine,
Romanian Reports in Physics 59, 289-299 (2007).
B. Mersch, N. Sela, G. Ast, S. Suhai and A. Hotz-Wagenblatt:
SERpredict: Detection of tissue- or tumor-specific isoforms generated through exonization of transposable elements,
BMC Genetics 8, 78 (2007). [doi:10.1186/1471-2156-8-78]
G. J. Halász, A. Vibók, S. Suhai and M. Baer:
The electronic nonadiabatic coupling term: Can it be ignored in dynamic calculations?,
J. Chem. Phys. 127, 244101-1 – 244101-8 (2007).
P. K. Shukla, P. C. Mishra and S. Suhai:
Reactions of DNA bases with the anti-cancer nitrogen mustard mechlorethamine: A quantum chemical study,
Chem. Phys. Lett. 449, 323-328 (2007).
F. Pingitore, C. Bleiholder, B. Paizs and C. Wesdemiotis:
Unimolecular chemistry of metal ion-coordinated alpha-dipeptide radicals,
Int. J. Mass Spectrom. 265, 251-260 (2007).
B. J. Bythell, D. F. Barofsky, F. Pingitore, M. J. Polce, P. Wang, C. Wesdemiotis and B. Paizs:
Backbone cleavages and sequential loss of carbon monoxide and ammonia from protonated AGG: A combined tandem mass spectrometry, isotope labeling, and theoretical study,
J. Am. Soc. Mass Spectrom. 18, 1291-1303 (2007).
N. Sela, B. Mersch, N. Gal-Mark, G. Lev-Maor, A. Hotz-Wagenblatt and G. Ast:
Comparative analysis of transposed element insertion within human and mouse genomes reveals Alus’s unique role in shaping the human transcriptome,
Genome Biol. 8, R127 (2007). [doi: 10.1186/gb-2007-8-6-r127]
C. Igel, T. Glasmachers, B. Mersch, N. Pfeifer and P. Meinicke:
Gradient-based optimization of kernel-target alignment for sequence kernels applied to bacterial gene start detection,
IEEE/ACM Transactions on Computational Biology and Bioinformatics 4, 216-226 (2007).
M. Kenzelmann, S. Maertens, M. Hergenhahn, S. Kueffer, A. Hotz-Wagenblatt, L. Li, S. Wang, C. Ittrich, T. Lemberger, R. Arribas, S. Jonnakuty, M. C. Hollstein, W. Schmid, N. Gretz, H. J. Gröne and G. Schütz:
Microarray analysis of newly synthesized RNA in cells and animals,
Proc. Natl. Acad. Sci. USA 104, 6164-6169 (2007).
T. A. Niehaus:
Mechanism of hydrogen bond assisted cis-trans isomerization in the excited state of 2-naphthol,
J. Chem. Phys. 126, 034303-1 – 034303-6 (2007).
C. S. Lin, R. Q. Zhang, T. A. Niehaus and Th. Frauenheim:
Geometric and electronic structures of carbon nanotubes adsorbed with flavin adenine dinucleotide: A theoretical study,
J. Phys. Chem. C 111, 4069-4073 (2007).
X. Wang, R. Q. Zhang, T. A. Niehaus and Th. Frauenheim:
Excited state properties of allylamine-capped silicon quantum dots,
J. Phys. Chem. C 111, 2394-2400 (2007).
X. Wang, R. Q. Zhang, S. T. Lee, T. A. Niehaus and Th. Frauenheim:
Unusual size dependence of the optical emission gap in small hydrogenated silicon nanoparticles,
Appl. Phys. Lett. 90, 123116-1 – 123116-3 (2007).
M. Elstner:
SCC-DFTB: What is the proper degree of self-consistency,
J. Phys. Chem. A 111, 5614-5621 (2007).
W. Waldeck, A. M. Strunz, G. Müller, A. Hotz-Wagenblatt, J. Wijenne, J. Langowski, B. Didinger, J. Debus and K. Braun:
Induced and repressed genes after irradiation sensitizing by pentoxyphylline,
Int. J. Cancer 120, 1198-1207 (2007).
D. Heringer, T. A. Niehaus, M. Wanko and Th. Frauenheim:
Analytical excited state forces for the time-dependent density-functional tight-binding method,
J. Comput. Chem. 28, 2589-2601 (2007).
Q. S. Li, R. Q. Zhang, S. T. Lee, T. A. Niehaus and Th. Frauenheim:
Stabilizing excited-state silicon nanoparticle by surface oxidation,
Appl. Phys. Lett. 91, 043106-1 – 043106-3 (2007).
X. Wang, R. Q. Zhang, T. A. Niehaus, Th. Frauenheim and S. T. Lee:
Hydrogenated silicon nanoparticles relaxed in excited states,
J. Phys. Chem. C 111, 12588-12593 (2007).
Q. S. Li, R. Q. Zhang, T. A. Niehaus, Th. Frauenheim and S. T. Lee:
Theoretical studies on optical and electronic properties of propionic-acid-terminated silicon quantum dots,
J. Chem. Theory Comput. 3, 1518- 1526 (2007).
B. Mersch, T. Glasmachers, P. Meinicke and C. Igel:
Evolutionary optimization of sequence kernels for detection of bacterial gene starts,
Int. J. of Neural Systems 17, 369-381 (2007).
C. Bleiholder, R. Gleiter, D. B. Werz and H. Köppel:
Theoretical investigations on heteronuclear chalcogen-chalcogen interactions: On the nature of weak bonds between chalcogen centers,
Inorg. Chem. 46, 2249-2260 (2007).
S. Gath, R. Gleiter, F. Rominger and C. Bleiholder:
Transannular interactions in mixed superphanes with one thiophene and one CpCo-stabilized cyclobutadiene ring: Syntheses, structures, and electrochemistry,
Organometallics 26, 644-650 (2007).
R. Gleiter, C. Bleiholder and F. Rominger:
Alpha-metallocenylmethylium ions and isoelectronic fulvene complexes of d6 to d9 metals. Structural considerations,
Organometallics 26, 4850-4859 (2007).
Y. Aoki, F. L. Gu, Y. Orimoto, S. Suhai and A. Imamura:
Elongation method applied to aperiodic systems - random polypeptides, high spin alignment, polymer in solvent, and DNA,
In “Computational Methods in Science and Engineering, Theory and Computation: Old Problems and New Challenges”, G. Maroulis and T. Simos (Eds.), American Institute of Physics, 2007, pp. 120-137.
HOCHSCHULSCHRIFTEN:
Dissertation von Christian Bleiholder: „Quantum Chemical Investigations on Gas Phase Chemistry of Protonated Peptides“,
Naturwissenschaftlich-Mathematische Gesamtfakultät, Universität Heidelberg, 2007, summa cum laude.
Dissertation von Bastien Chevreux: „MIRA: An Automated Genome and EST Assembler“,
Medizinische Fakultät, Universität Heidelberg, 2007, magna cum laude.
K. J. Jalkanen, V. Würtz-Jürgensen, A. Claussen, A. Rahim, G. M. Jensen, R. C. Wade, F. Nardi, C. Jung, I. M. Degtyarenko, R. M. Nieminen, F. Herrmann, M. Knapp-Mohammady, T. A. Niehaus, K. Frimand and S. Suhai:
Use of vibrational spectroscopy to study protein and DNA structure, hydration, and binding of biomolecules: A combined theoretical and experimental approach,
Int. J. Quant. Chem. 106, 1160-1198 (2006).
Á. Vibók, G. J. Halász, S. Suhai, D. K. Hoffman, D. J. Kouri and M. Baer:
Two-state versus three-state quantization: An ab initio study of the three lower states of the {N,H2| A'} system,
J. Chem. Phys. 124, 24312-1 – 24312-8 (2006).
P. Siedlecki, R. G. Boy, T. Musch, B. Brueckner, S. Suhai, F. Lyko and P. Zielenkiewicz:
Discovery of two novel, small-molecule inhibitors of DNA methylation,
J. Med. Chem. 49, 678-683 (2006).
A. Vinayagam, C. del Val, F. Schubert, R. Eils, K.-H. Glatting, S. Suhai and R. König:
GOPET: A tool for automated predictions of Gene Ontology terms,
BMC Bioinformatics 7, 161 (2006) [doi:10.1186/1471-2105-7-161].
A. Kumar, P. C. Mishra and S. Suhai:
Binding of gold clusters with DNA base pairs: A density functional study of neutral and anionic GC–Aun and AT–Aun (n = 4, 8) complexes,
J. Phys. Chem. 110, 7719-7727 (2006).
A. L. Hufton, A. Vinayagam, S. Suhai and J. C. Baker:
Genomic analysis of Xenopus organizer function,
BMC Developmental Biology 6, 27 (2006) [doi:10.1186/1471-213X-6-27].
A. G. Harrison, A. B. Young, C. Bleiholder, S. Suhai and B. Paizs:
Scrambling of sequence information in collision-induced dissociation of peptides,
J. Am. Chem. Soc. 128, 10364-10365 (2006).
N. H. March, T. A. Niehaus and S. Suhai:
Influence of the noninteracting density response function on the exchange-only kernel in time-dependent density-functional theory,
Phys. Rev. A 74, 044502-1 – 044502-3 (2006).
C. del Val, V. Y. Kuryshev, K-H. Glatting, P. Ernst, A. Hotz-Wagenblatt, A. Poustka, S. Suhai and S. Wiemann:
CAFTAN: a tool for fast mapping, and quality assessment of cDNAs,
BMC Bioinformatics 7, 473 (2006) [doi:10.1186/1471-2105-7-473].
C. Bleiholder, S. Suhai and B. Paizs:
Revising the proton affinity scale of the naturally occurring α-amino acids,
J. Am. Soc. Mass Spectrom. 17, 1275-1281 (2006).
N. H. March, Zs. Jánosfalvi, Á. Nagy and S. Suhai:
Kinetic and exchange energy related non-locally in Hartree-Fock theory of an inhomogeneous electron liquid,
Phys. & Chem. of Liquids 44, 493-499 (2006).
T. Cooper, E. Talaty, J. Grove, M. Van Stipdonk, S. Suhai and B. Paizs:
Isotope labeling and theoretical study of the formation of a3* ions from protonated tetraglycine,
J. Am. Soc. Mass Spectrom. 17, 1654-1664 (2006).
C. Bleiholder, D. B. Werz, H. Köppel and R. Gleiter:
Theoretical investigations on chalcogen-chalcogen interactions: What makes these nonbonded interactions bonding?,
J. Am. Chem. Soc. 128, 2666-2674 (2006).
M. Hackenberg, Ch. Previti, P. L. Luque-Escamilla, P. Carpena, J. Martínez-Aroza and J. L. Oliver:
CpGcluster: a distance-based algorithm for CpG-island detection,
BMC Bioinformatics 7, 446 (2006) [doi:10.1186/1471-2105-7-446].
S. Laufs, G. Guenechea, A. Gonzalez-Murillo, K. Z. Nagy, M. L. Lozano, C. del Val, S. Jonnakuty, A. Hotz-Wagenblatt, W. J. Zeller, J. A. Bueren and S. Fruehauf:
Lentiviral vector integration sites in human NOD/SCID repopulating cells,
J. Gene Med. 8, 1197-1207 (2006).
F. A. Giordano, B. Fehse, A. Hotz-Wagenblatt, S. Jonnakuty, C. del Val, J.-U. Appelt, K. Z. Nagy, K. Kuehlcke, S. Naundorf, A. R. Zander, W. J. Zeller, A. D. Ho, S. Fruehauf and S. Laufs:
Retroviral vector insertions in T-lymphocytes used for suicide gene therapy occur in gene groups with specific molecular functions,
Bone Marrow Transplantation 38, 229-235 (2006).
A. Mehrle, H. Rosenfelder, I. Schupp, C. del Val, D. Arlt, F. Hahne, S. Bechtel, J. Simpson, O. Hofmann, W. Hide, K.-H. Glatting, W. Huber, R. Pepperkok, A. Poustka and S. Wiemann:
The LIFEdb database in 2006,
Nuc. Acids Res. 34, Database issue, D415-D418 (2006).
P. Wang, M. J. Polce, C. Bleiholder, B. Paizs and C. Wesdemiotis:
Structural characterization of peptides via tandem mass spectrometry of their dilithiated monocations,
Int. J. Mass Spectrom. 249-250, 45-59 (2006).
D. B. Werz, C. Bleiholder, R. Gleiter and F. Rominger:
Strong distortions in hexacarbonyldicobalt complexes by push-pull effects,
J. Organomet. Chem. 691, 3943-3947 (2006).
M. Elstner:
The SCC-DFTB method and its application to biological systems,
Theor. Chem. Acc. 116, 316-325 (2006).
M. Wanko, M. Hoffmann, T. Frauenheim and M. Elstner:
Computational photochemistry of retinal proteins,
J. Comput. Aided Mol. Des. 20, 511-518 (2006).
M. Hoffmann, M. Wanko, P. Strodel, P. H. König, T. Frauenheim, K. Schulten, W. Thiel, E. Tajkhorshid and M. Elstner:
Color tuning in rhodopsins: The mechanism for the spectral shift between bacteriorhodopsin and sensory rhodopsin II,
J. Am. Chem. Soc. 128, 10808-10818 (2006).
D. Riccardi, P. Schaefer, Y. Yang, H. Yu, N. Ghosh, X. Prat-Resina, P. König, G. Li, D. Xu, H. Guo, M. Elstner and Q. Cui:
Development of effective quantum mechanical/molecular mechanical (QM/MM) methods for complex biological processes,
J. Phys. Chem. B 110, 6458-6469 (2006).
F. A. Giordano, B. Fehse, A. Hotz-Wagenblatt, S. Jonnakuty, C. del Val, J.-U. Appelt, K. Z. Nagy, K. Kuehlcke, S. Naundorf, A. R. Zander, W. J. Zeller, A. D. Ho, S. Fruehauf and S. Laufs:
Retroviral vector insertions in T-lymphocytes used for suicide gene therapy occur in gene groups with specific molecular functions,
Bone Marrow Transplant. 38, 229-235 (2006).
B. Mersch, T. Glasmachers, P. Meinicke and C. Igel:
Evolutionary optimization of sequence kernels for detection of bacterial gene starts,
In “ICANN 2006, Part II, LNCS 4132”,
S. Kollias et al. (Eds.), Springer, Berlin Heidelberg, 2006, pp. 827-836.
HOCHSCHULSCHRIFTEN:
Dissertation von Vinayagam Arunachalam: „Strategies for automatic genome annotation“,
Medizinische Fakultät, Universität Heidelberg, 2006, magna cum laude.
A. N. Bondar, M. Elstner, S. Suhai, S. Fischer and J. C. Smith:
Direct proton transfer in a putative L-state intermediate of the bacteriorhodopsin photocycle,
Phase Transitions 78, 5-9 (2005).
A. Bende, Á. Vibók, G. J. Halász and S. Suhai:
Theoretical study of hydrogen bonds between acetylene and selected proton donor systems,
Int. J. Quant. Chem. 101, 186-200 (2005).
P. C. Mishra, A. K. Singh and S. Suhai:
Interaction of singlet oxygen and superoxide radical anion with guanine and formation of its mutagenic modification 8-oxoguanine,
Int. J. Quant. Chem. 102, 282-301 (2005).
B. Paizs and S. Suhai:
Fragmentation pathways of protonated peptides,
Mass Spectrom. Rev. 24, 508-548 (2005).
A. Bende and S. Suhai:
BSSE-corrected geometry and harmonic and anharmonic vibrational frequencies of formamide-water and formamide-formamide dimers,
Int. J. Quant. Chem. 103, 841-853 (2005).
N. C. Polfer, B. Paizs, L. C. Snoek, I. Compagnon, S. Suhai, G. Meijer, G. von Helden and J. Oomens:
Infrared fingerprint spectroscopy and theoretical studies of potassium ion tagged amino acids and peptides in the gas phase,
J. Am. Chem. Soc. 127, 8571-8579 (2005).
B. Brueckner, R. G. Boy, P. Siedlecki, T. Musch, H. C. Kliem, P. Zielenkiewicz, S. Suhai, M. Wiessler and F. Lyko:
Epigenetic reactivation of tumor suppressor genes by a novel small-molecule inhibitor of human DNA methyltransferases,
Cancer Res. 65, 6305-6311 (2005).
A.-N. Bondar, S. Fischer, S. Suhai and J. C. Smith:
Tuning of retinal twisting in bacteriorhodopsin controls the directionality of the early photocycle steps,
J. Phys. Chem. B Lett. 109, 14786-14788 (2005).
Á. Vibók, G. J. Halász, S. Suhai and M. Baer:
Assigning signs to the electronic nonadiabatic coupling terms: The {H2,O} system as a case study,
J. Chem. Phys. 122, 134109-1 – 134109-8 (2005).
A. Kumar, P. C. Mishra and S. Suhai:
Adiabatic electron affinities of the polyhydrated adenine-thymine base pair:
A density functional study,
J. Phys. Chem. A 109, 3971-3979 (2005).
N. C. Polfer, J. Oomens, S. Suhai and B. Paizs:
Spectroscopic and theoretical evidence for oxazolone ring formation in collision-induced dissociation of peptides,
J. Am. Chem. Soc. 127, 17154-17155 (2005).
T. L. Schmitt, A. Hotz-Wagenblatt, H. Klein and W. Dröge:
Interdependent regulation of insulin receptor kinase activity by ADP and hydrogen peroxide,
J. Biol. Chem. 280, 3795-3801 (2005).
T. A. Niehaus, M. Rohlfing, F. Della Sala, A. Di Carlo and Th. Frauenheim:
Quasiparticle energies for large molecules: A tight-binding-based Green’s-function approach,
Phys. Rev. A 71, 22508-1 – 22508-10 (2005).
D. Baldessari, Y. Shin, O. Krebs, R. König, T. Koide, A. Vinayagam, U. Fenger, M. Mochii,C. Terasaka, A. Kitayama, D. Pfeiffer, N. Ueno, R. Eils, K. W. Cho and C. Niehrs:
Global gene expression profiling and cluster analysis in Xenopus laevis,
Mechanisms of Development 122, 441-475 (2005).
M. Wanko, M. Hoffmann, P. Strodel, A. Koslowski, W. Thiel, F. Neese, T. Frauenheim and M. Elstner:
Calculating absorption shifts for retinal proteins: Computational challenges,
J. Phys. Chem. B 109, 3606-3615 (2005).
T. A. Niehaus, D. Heringer, B. Torralva and Th. Frauenheim:
Importance of electronic self-consistency in the TDDFT based treatment of
nonadiabatic molecular dynamics,
Eur. Phys. J. D 35, 467-477 (2005).
S. I. Simdyankin, M. Elstner, T. A. Niehaus, Th. Frauenheim and S. R. Elliott:
Influence of copper on the electronic properties of amorphous chalcogenides,
Phys. Rev. B 72, 020202-1 – 020202-4 (2005).
T. Krüger, M. Elstner, P. Schiffels and Th. Frauenheim:
Validation of the density-functional based tight-binding approximation method for the calculation of reaction energies and other data,
J. Chem. Phys. 122, 114110-1 – 114110-5 (2005).
C. S. Lin, R. Q. Zhang, S. T. Lee, M. Elstner, Th. Frauenheim and L. J. Wan:
Simulation of water cluster assembly on a graphite surface,
J. Phys. Chem. B 109, 14183-14188 (2005).
H. Mehrez, A.Svizenko, M. P. Anantram, M. Elstner and T. Frauenheim:
Analysis of band-gap formation in squashed armchair carbon nanotubes,
Phys. Rev. B 71, 155421-1 – 155421-7 (2005).
K. Range, D. Riccardi, Q. Cui, M. Elstner and D. M. York:
Benchmark calculations of proton affinities and gas-phase basicities of molecules important in the study of biological phosphoryl transfer,
Phys. Chem. Chem. Phys. 7, 3070 (2005).
Zs. Jánosfalvi, K. D. Sen and Á. Nagy:
Cusp conditions for non-interacting kinetic energy density of the density functional theory,
Phys. Lett. A 344, 1-6 (2005).
J. Derbinski, J. Gäbler, B. Brors, S. Tierling, S. Jonnakuty, M. Hergenhahn, L. Peltonen, J. Walter and B. Kyewski:
Promiscuous gene expression in thymic epithelial cells is regulated at multiple levels,
J. Exp. Med. 202, 33-45 (2005).
A. Vinayagam, C. del Val, R. König, F. Schubert, R. Eils, K.-H. Glatting and S. Suhai:
GOPET: a tool for automatic Gene Ontology term prediction,
Proceedings of the First AFP SIG in ISMB 2005: Detroit, MI, 37-38 (2005).
S. Irle, G. Zheng, M. Elstner and K. Morokuma:
High-temperature quantum chemical molecular dynamics simulations of carbon
nanostructure self-assembly processes,
in “Theory and Applications of Computational Chemistry: The First 40 Years”,
Eds. C. E. Dykstra, G. Frenking, K. S. Kim, G. E. Scuseria,Elsevier, pp. 875-889 (2005).
HOCHSCHULSCHRIFTEN:
Dissertation von Peter Ernst: „Complex analysis pipelines in bioinformatics“,
Medizinische Fakultät, Universität Heidelberg, 2005, magna cum laude.
Dissertation von Michaela Knapp-Mohammady: „Kooperative Effekte in der Strukturbildung von Biomolekülen“,
Medizinische Fakultät, Universität Heidelberg, 2005, magna cum laude.
N. Bondar, M. Elstner, S. Fischer, J. C. Smith and S. Suhai:
Can coordinate driving describe proton transfer coupled to complex protein motions?
Phase Transitions 77, 47-52 (2004).
T. Crass, I. Antes, R. Basekow, P. Bork, C. Buning, M. Christensen, H. Claußen, C. Ebeling, P. Ernst, V. Gailus-Durner, K.-H. Glatting, R. Gohla, F. Gößling, K. Grote, K. Heidtke, A. Herrmann, S. O’Keeffe, O. Kießlich, S. Kolibal, J. O. Korbel, T. Lengauer, I. Liebich, M. van der Linden, H. Luz, K. Meissner, C. von Mering, H.-T. Mevissen, H.-W. Mewes, H. Michael, M. Mokrejs, T. Müller, H. Pospisil, M. Rarey, J. G. Reich, R. Schneider, D. Schomburg, S. Schulze-Kremer, K. Schwarzer, I. Sommer, S. Springstubbe, S. Suhai, G. Thoppae, M. Vingron, J. Warfsmann, T. Werner, D. Wetzler, E. Wingender and R. Zimmer:
The Helmholtz Network for Bioinformatics: an integrative web portal for
bioinformatics resources,
Bioinformatics 20, 268-270 (2004).
C. del Val, A. Mehrle, M. Falkenhahn, M. Seiler, K.-H. Glatting, A. Poustka, S. Suhai and S. Wiemann:
High-throughput protein analysis integrating bioinformatics and experimental assays,
Nuc. Acids Res. 32, 742-748 (2004).
K. J. Jalkanen, M. Elstner and S. Suhai:
Amino acids and small peptides as building blocks for proteins: comparative
theoretical and spectroscopic studies,
J. Mol. Struct. (Theochem) 675, 61-77 (2004).
A. Kumar, M. Knapp-Mohammady, P.C. Mishra and S. Suhai:
A theoretical study of structures and electron affinities of radical anions of guanine-cytosine, adenine-thymine, and hypoxanthine-cytosine base pairs,
J. Comput. Chem. 25, 1047-1059 (2004).
I. Mayer, M. Knapp-Mohammady and S. Suhai:
Bond orders and energy components in polymers,
Chem. Phys. Lett. 389, 34-38 (2004).
B. Paizs and S. Suhai:
Towards understanding the tandem mass spectra of protonated oligopeptides. 1:
Mechanism of amide bond cleavage,
J. Am. Soc. Mass Spectrom. 15, 103-113 (2004).
B. Paizs, M. Schnölzer, U. Warnken, S. Suhai and A. G. Harrison:
Cleavage of the amide bond of protonated dipeptides,
Phys. Chem. Chem. Phys. 6, 2691-2699 (2004).
P. Kolandaivel, M. Knapp-Mohammady and S. Suhai:
Studies on structure and conformational stability of free canonical 2'-
deoxyribonucleosides: Approximate SCC-DFTB and LMP2 methods,
Int. J. Quant. Chem. 99, 28-38 (2004).
B. Chevreux, T. Pfisterer, B. Drescher, A. J. Driesel, W. E. G. Müller, T. Wetter and S. Suhai:
Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs,
Genome Research 14, 1147-1159 (2004).
A.-N. Bondar, M. Elstner, S. Suhai, J. C. Smith and S. Fischer:
Mechanism of primary proton transfer in bacteriorhodopsin,
Structure 12, 1281-1288 (2004).
M. Baer, T. Vértesi, G. J. Halász, Á. Vibók and S. Suhai:
On diabatization and the topological D-matrix: Theory and numerical studies of the H + H2 system and the C2H2 molecule,
Faraday Discuss. 127, 337-353 (2004).
I. P. Csonka, B. Paizs and S. Suhai:
Modeling of the gas-phase ion chemistry of protonated arginine,
J. Mass Spectrom. 39, 1025-1035 (2004).
I. A. Howard, D. J. Klein, N. H. March, C. Van Alsenoy, S. Suhai, Z. Jánosvalfi and Á. Nagy:
Change in electronic structure of polyenes due to interaction with polyacenes and with graphitic strips,
J. Phys. Chem. B 108, 14870-14875 (2004).
A. Vinayagam, R. König, J. Moormann, F. Schubert, R. Eils, K.-H. Glatting and S. Suhai:
Applying Support Vector Machines for Gene ontology based gene function prediction,
BMC Bioinformatics 5, 116-129 (2004).
A. Bende, Á. Vibók, G. J. Halász and S. Suhai:
Ab initio study of the ammonia-ammonia dimer: BSSE-free structures and
intermolecular harmonic vibrational frequencies,
Int. J. Quant. Chem. 99, 585-593 (2004).
A.-N. Bondar, S. Fischer, J. C. Smith, M. Elstner and S. Suhai:
Key role of electrostatic interactions in bacteriorhodopsin proton transfer,
J. Am. Chem. Soc. 126, 14668-14677 (2004).
T. Vértesi, Á. Vibók, G. J. Halász and M. Baer:
On the peculiarities of the diabatic framework: New insight,
J. Chem. Phys. 120, 2565-2574 (2004).
I. Jelcic, A. Hotz-Wagenblatt, A. Hunziker, H. zur Hausen and E.-M. de Villiers:
Isolation of multiple TT virus genotypes from spleen biopsy tissue from a Hodgkin’s disease patient: Genome reorganization and diversity in the hypervariable region,
J. of Virology 78, 7498-7507 (2004).
A. Jegorov, B. Paizs, M. Kuzma, M. Zabka, Z. Landa, M. Sulc, M. P. Barrow and V.Havlicek:
Extraribosomal cyclic tetradepsipeptides beauverolides: profiling and modeling the fragmentation pathways,
J. Mass Spectrom. 39, 949-960 (2004).
M. Wanko, M. Garavelli, F. Bernardi, T. A. Niehaus, T. Frauenheim and M. Elstner:
A global investigation of excited state surfaces within time-dependent density-functional response theory,
J. Chem. Phys. 120, 1674-1692 (2004).
S. Laufs, K. Z. Nagy, F. A. Giordano, A. Hotz-Wagenblatt, W. J. Zeller, S. Fruehauf:
Insertion of retroviral vectors in NOD/SCID repopulating human peripheral blood progenitor cells occurs preferentially in the vicinity of transcription start regions and in introns,
Mol. Therapy 10, 874-881 (2004).
G. Fagas, A. Kambili and M. Elstner:
Complex-band structure: a method to determine the off-resonant electron transport in oligomers,
Chem. Phys. Lett. 389, 268-273 (2004).
G. S. Zheng, S. Irle, M. Elstner and K. Morokuma:
Quantum chemical molecular dynamics model study of fullerene formation from
open-ended carbon nanotubes,
J. Phys. Chem. A 108, 3182-3194 (2004).
T. Okada, M. Sugihara, A.-N. Bondar, M. Elstner, P. Entel and V. Buss:
The retinal conformation and its environment in rhodopsin in light of a new 2.2 Å crystal structure,
J. Mol. Biol. 342, 571-583 (2004).
A. Vinayagam, G. Pugalenthi, R. Rajesh and R. Sowdhamini:
DSDBASE: a consortium of native and modelled disulphide bonds in proteins, Nuc. Acids Res. 32, D200-D202 (2004).
D. Bannasch, A. Mehrle, K.-H. Glatting, R. Pepperkok, A. Poustka and S. Wiemann:
LIFEdb: a database for functional genomics experiments integrating information from external sources, and serving as a sample tracking system,
Nuc. Acids Res. 32, D505-D508 (2004).
HOCHSCHULSCHRIFTEN:
Dissertation von Ana-Nicoleta Bondar: „Active ion transport across cellular membranes: The mechanism of the bacteriorhodopsin proton pump“,
Universität Heidelberg, Fakultät für Biowissenschaften, 2004, summa cum laude.
P. Ernst, K.-H. Glatting and S. Suhai:
A task framework for the web interface W2H,
Bioinformatics 19, 278-282 (2003).
A. Bende, M. Knapp-Mohammady and S. Suhai:
BSSE-free description of intermolecular force constants in hydrogen fluoride and water dimers,
Int. J. Quant. Chem. 92, 152-159 (2003).
K. J. Jalkanen, R. M. Nieminen, M. Knapp-Mohammady and S. Suhai:
Vibrational analysis of various isotopomers of L-alanyl-L-alanine in aqueous solution: Vibrational absorption, vibrational circular dichroism, Raman and Raman optical activity spectra,
Int. J. Quant. Chem. 92, 239-259 (2003).
S. Abdali, T. A. Niehaus, K. J. Jalkanen, X. Cao, L. A. Nafie, Th. Frauenheim, S. Suhai and H. Bohr:
Vibrational absorption spectra, DFT and SCC-DFTB conformational study and
analysis of [Leu]enkephalin,
Phys. Chem. Chem. Phys. 5, 1295-1300 (2003).
O. V. Shishkin, L. Gorb, A. V. Luzanov, M. Elstner, S. Suhai and J. Leszczynski:
Structure and conformational flexibility of uracil: A comprehensive study of
performance of the MP2, B3LYP and SCC-DFTB methods,
J. Mol. Struct. (Theochem) 625, 295-303 (2003).
P. Siedlecki, R. G. Boy, S. Comagic, R. Schirrmacher, M. Wiessler, P. Zielenkiewicz, S. Suhai and F. Lyko:
Establishment and functional validation of a structural homology model for human DNA methyltransferase 1,
Biochem. and Biophys. Res. Commun. 306, 558-563 (2003).
A. Hotz-Wagenblatt, T. Hankeln, P. Ernst, K.-H. Glatting, E. R. Schmidt and S. Suhai:
ESTAnnotator: a tool for high throughput EST annotation,
Nuc. Acids Res. 31, 3716-3719 (2003).
A. Kumar, M. Elstner and S. Suhai:
SCC-DFTB-D study of intercalating carcinogens: Benzo(a)pyrene and its metabolites complexed with the G-C base pair,
Int. J. Quant. Chem. 95, 44-59 (2003).
M. Elstner, T. Frauenheim and S. Suhai:
An approximate DFT method for QM/MM simulations of biological structures and
processes,
J. Mol. Struct. (Theochem) 632, 29-41 (2003).
T. Wyttenbach, B. Paizs, P. Barran, L. Breci, D. Liu, S. Suhai, V. H. Wysocki and M. T. Bowers:
The effect of the initial water of hydration on the energetics, structures, and H/D-exchange mechanism of a family of pentapeptides: An experimental and theoretical study,
J. Am. Chem. Soc. 125, 13768-13775 (2003).
Á. Vibók, G. J. Halász, T. Vértesi, S. Suhai, M. Baer and J. P. Toennies:
Ab-initio conical intersections for the Na+H2 system: A four-state study,
J. Chem. Phys. 119, 6588- 6596 (2003).
C. del Val, K.-H. Glatting and S. Suhai:
cDNA2Genome: A tool for mapping and annotating cDNAs,
BMC Bioinformatics 4, 39-46 (2003).
B. Paizs, S. Suhai and A. G. Harrison:
Experimental and theoretical investigation of the main fragmentation pathways of protonated H-Gly-Gly-Sar-OH and H-Gly-Sar-Sar-OH,
J. Am. Soc. Mass Spectrom. 14, 1454-1469 (2003).
O. V. Shishkin, M. Elstner, T. Frauenheim and S. Suhai:
Structure of stacked dimers of N-methylated Watson-Crick adenine-thymine base
pairs,
Int. J. Mol. Sci. 4, 537-547 (2003).
T. Vértesi, Á. Vibók, G. J. Halász, A. Yahalom, R. Englman and M. Baer:
The electronic non-adiabatic coupling matrix: A numerical study of the curl condition and the quantization condition employing the Mathieu equation,
J. Phys. Chem. A 107, 7189-7196 (2003).
M. Muckenthaler, A. Richter, N. Gunkel, D. Riedel, M. Polycarpou-Schwarz, S. Hentze, M. Falkenhahn, W. Stremmel, W. Ansorge and M. W. Hentze:
Relationships and distinctions in iron-regulatory networks responding to interrelated signals,
Blood 101, 3690-3698 (2003).
A. Jegorov, B. Paizs, M. Žabka, M. Kuzma, V. Havlíček, A. E. Giannakopulos and P. J. Derrick:
Profiling of cyclic hexadepsipeptides roseotoxins synthesized in vitro and in vivo: a combined tandem mass spectrometry and quantum chemical study,
Eur. J. Mass Spectrom. 9, 105-116 (2003).
F. Tasnádi and Á. Nagy:
Study of subspace density functional theory application of LSDA to excited states of atoms,
Int. J. Quant. Chem. 92, 234-238 (2003).
F. Tasnádi and Á. Nagy:
An approximation to the ensemble Kohn-Sham exchange potential for excited states of atoms,
J. Chem. Phys. 119, 4141-4147 (2003).
F. Tasnádi and Á. Nagy:
Ghost- and self-interaction-free ensemble calculations with local exchange-correlation potential for atoms,
J. Phys. B 36, 4073-4080 (2003).
S. Irle, G. S. Zheng, M. Elstner and K. Morokuma:
Formation of fullerene molecules from carbon nanotubes: A quantum chemical
molecular dynamics study,
Nano Letters 3, 465-470 (2003).
S. Irle, G. S. Zheng, M. Elstner and K. Morokuma:
From C2 molecules to self-assembled fullerenes in quantum chemical molecular
dynamics,
Nano Letters 3, 1657-1664 (2003).
A. Vinayagam, J. Shi, G. Pugalenthi, B. Meenakshi, T. L. Blundell and R. Sowdhamini:
DDBASE2.0: updated domain database with improved identification of structural
domains,
Bioinformatics 19, 1760-1764 (2003).
HOCHSCHULSCHRIFTEN:
Dissertation von Christof Köhler: „Berücksichtigung von Spinpolarisationseffekten in einem dichtefunktionalbasierten Ansatz“,
Universität Paderborn, Fakultät für Naturwissenschaften, Department Physik, 2003, mit Auszeichnung.
B. Paizs and S. Suhai:
Combined quantum chemical and RRKM modeling of the main fragmentation pathways of protonated GGG. II. Formation of b2, y1, and y2 ions,
Rapid Commun. Mass Spectrom. 16, 375-389 (2002).
Th. Frauenheim, G. Seifert, M. Elstner, T. Niehaus, C. Köhler, M. Amkreutz, M. Sternberg,
Z. Hajnal, A. Di Carlo and S. Suhai:
Atomistic simulations of complex materials: ground-state and excited-state properties,
J. Phys.: Condens. Matter 14, 3015-3047 (2002).
H. Zhou, E. Tajkhorshid, Th. Frauenheim, S. Suhai and M. Elstner:
Performance of the AM1, PM3, and SCC-DFTB methods in the study of conjugated Schiff base molecules,
Chem. Phys. 277, 91-103 (2002).
C. d. Val, P. Ernst, R. Bräuning, K.-H. Glatting and S. Suhai:
PATH: a task for the inference of phylogenies,
Bioinformatics 18, 646-647 (2002).
B. Paizs, S. Suhai, B. Hargittai, V. J. Hruby and Á. Somogyi:
Ab initio and MS/MS studies on protonated peptides containing basic and acidic amino acid residues. I. Solvated proton vs. salt-bridged structures and the cleavage of the terminal amide bond of protonated RD-NH2,
Int. J. Mass Spectrom. 219, 203-232 (2002).
B. Paizs and S. Suhai:
Towards understanding some ion intensity relationships for the tandem mass spectra of protonated peptides,
Rapid Commun. Mass Spectrom. 16, 1699-1702 (2002).
S. Abdali, K. J. Jalkanen, H. Bohr, S. Suhai and R. M. Nieminen:
The VA and VCD spectra of various isotopomers of L-alanine in aqueous solution,
Chem. Phys. 282, 219-235 (2002).
G. J. Halász, Á. Vibók, S. Suhai and I. Mayer:
Toward a BSSE-free description of strongly interacting systems,
Int. J. Quant. Chem. 89, 190-197 (2002).
D. Reha, M. Kabelác, F. Ryjácek, J. Sponer, J. E. Sponer, M. Elstner, S. Suhai and P.Hobza:
Intercalators. 1. Nature of stacking interactions between intercalators (ethidium, daunomycin, ellipticine, and 4’,6-diaminide-2-phenylindole) and DNA base pairs. Ab initio quantum chemical, density functional theory, and empirical potential study,
J. Am. Chem. Soc. 124, 3366-3376 (2002).
P. Pulay and B. Paizs:
Newtonian molecular dynamics in general curvilinear internal coordinates,
Chem. Phys. Lett. 353, 400-406 (2002).
K. Frimand and K. J. Jalkanen:
SCC-TB, DFT/B3LYP, MP2, AM1, PM3 and RHF study of ethylene oxide and
propylene oxide structures, VA and VCD spectra,
Chem. Phys. 279, 161-178 (2002).
P. Bobadova-Parvanova, K. A. Jackson, S. Srinivas, M. Horoi, C. Köhler and G. Seifert:
Scanning the potential energy surface of iron clusters: A novel search strategy,
J. Chem. Phys. 116, 3576-3587 (2002).
F. Tasnádi and Á. Nagy:
Local self-interaction-free approximate exchange-correlation potentials in the variational density functional theory for individual excited states,
Chem. Phys. Lett. 366, 496-503 (2002).
A. Hotz-Wagenblatt and W. Dröge:
Redox-mediated functional and structural changes in insulin receptor kinase,
In: Protein Sensors and Reactive Oxygen Species, Pt B,
Thiol Enzymes and Proteins (Methods in Enzymology) 348, 288-296 (2002).
J. Fabian, L. A. Diaz, G. Seifert and T. Niehaus:
Calculation of excitation energies of organic chromophores: a critical evaluation,
J. Mol. Struct. (Theochem) 594, 41-53 (2002).
D. Margetis, E. Kaxiras, M. Elstner, Th. Frauenheim and M. R. Manaa:
Electronic structure of solid nitromethane: Effects of high pressure and molecular vacancies,
J. Chem. Phys. 117, 788-799 (2002).
P. Maragakis, R. L. Barnett, E. Kaxiras, M. Elstner and T. Frauenheim:
Electronic structure of overstretched DNA,
Phys. Rev. B 66, art-241104 (2002).
M. Gumbel, R. Grebe, M. Knapp-Mohammady, G. M. Ullmann und J. Langowski:
Modellierung biologischer Prozesse,
In „Handbuch der Medizinischen Informatik“, T. M. Lehmann und E. Meyer zu Bexten, Hrsg., Hanser, München, Wien, 2002, S. 169-223.
T. A. Niehaus, M. Elstner, Th. Frauenheim and S. Suhai:
Application of an approximate density-functional method to sulfur containing compounds,
J. Mol. Struct. (THEOCHEM) 541, 185-194 (2001).
B. Paizs, P. Salvador, A. G. Császár, M. Duran and S. Suhai:
Intermolecular bond lengths: extrapolation to the basis set limit on uncorrected and BSSE-corrected potential energy hypersurfaces,
J. Comp. Chem. 22, 196-207 (2001).
M. Elstner, K. J. Jalkanen, M. Knapp-Mohammady, T. Frauenheim and S. Suhai:
Energetics and structure of glycine and alanine based model peptides: Approximate SCC-DFTB, AM1 and PM3 methods in comparison with DFT, HF and MP2 calculations,
Chem. Phys. 263, 203-219 (2001).
K. J. Jalkanen, R. M. Nieminen, K. Frimand, J. Bohr, H. Bohr, R. C. Wade, E.
Tajkhorshid and S. Suhai:
A comparison of aqueous solvent models used in the calculation of the Raman and ROA spectra of L-alanine,
Chem. Phys. 265, 125-151 (2001).
S. W. Bunte, G. M. Jensen, K. L. McNesby, D. B. Goodin, C. F. Chabalowski, R. M. Nieminen, S. Suhai and K. J. Jalkanen:
Theoretical determination of the vibrational absorption and Raman spectra of 3-methylindole and 3-methylindole radicals,
Chem. Phys. 265, 13-25 (2001).
M. Elstner, P. Hobza, T. Frauenheim, S. Suhai and E. Kaxiras:
Hydrogen bonding and stacking interactions of nucleic acid base pairs: A density-functional-theory based treatment,
J. Chem. Phys. 114, 5149-5155 (2001).
P. Salvador, B. Paizs, M. Duran and S. Suhai:
On the effect of the BSSE on intermolecular potential energy surfaces. Comparison of a priori and a posteriori BSSE correction schemes,
J. Comp. Chem. 22, 765-786 (2001).
B. Paizs, I. P. Csonka, G. Lendvay and S. Suhai:
Proton mobility in protonated glycylglycine and N-formylglycylglycinamide: a combined quantum chemical and RKKM study,
Rapid Commun. Mass Spectrom. 15, 637-650 (2001).
B. Paizs and S. Suhai:
Theoretical study of the main fragmentation pathways for protonated glycylglycine,
Rapid Commun. Mass Spectrom. 15, 651-663 (2001).
T. A. Niehaus, S. Suhai, F. Della Sala, P. Lugli, M. Elstner, G. Seifert and
Th. Frauenheim:
Tight-binding approach to time-dependent density-functional response theory,
Phys. Rev. B 63, 85108-1 – 85108-9 (2001).
L. Edler, J. Grassmann and S. Suhai:
Role and results of statistical methods in protein fold class prediction,
Math. and Comp. Modelling 33, 1401-1417 (2001).
H. G. Bohr, K. Frimand, K. J. Jalkanen, R. M. Nieminen and S. Suhai:
Neural-network analysis of the vibrational spectra of N-acetyl L-alanyl N’-methyl amide conformational states,
Phys. Rev. E 64, 21905-1 - 21905-13 (2001).
B. Paizs and S. Suhai:
Combined quantum chemical and RRKM modeling of the main fragmentation pathways of protonated GGG. I. Cis-trans isomerization around protonated amide bonds,
Rapid Commun. Mass Spectrom. 15, 2307-2323 (2001).
C. Köhler, Z. Hajnal, P. Deák, Th. Frauenheim and S. Suhai:
Theoretical investigation of carbon defects and diffusion in -quartz,
Phys. Rev. B 64, 85333-1 – 85333-7 (2001).
B. Torralva, T. A. Niehaus, M. Elstner, S. Suhai, Th. Frauenheim and R. E. Allen:
Response of C60 and Cn to ultrashort laser pulses,
Phys. Rev. B 64, 153105-1 – 153105-4 (2001).
C. Köhler, G. Seifert, U. Gerstmann, M. Elstner, H. Overhof and Th. Frauenheim:
Approximate density-functional calculations of spin densities in large molecular systems and complex solids,
PCCP 3, 5109-5114 (2001).
R. Bräuning, M. van der Linden, B. Pardon und S. Suhai:
Bioinformatik – Lichtblick am Ende des Datentunnels?
Biospektrum 1, 72-75 (2001).
Q. Cui, M. Elstner, E. Kaxiras, Th. Frauenheim and M. Karplus:
A QM/MM implementation of the self-consistent charge density functional tight binding (SCC-DFTB) method:
J. Phys. Chem. B 105, 569 – 585 (2001).
E. Kim, C. Chen, T. Köhler, M. Elstner and Th. Frauenheim:
Tetragonal crystalline carbon nitrides: Theoretical predictions,
Phys. Rev. Lett. 86, 652 – 655 (2001).
J. Widany, G. Daminelli, A. Di Carlo, P. Lugli, G. Jungnickel, M. Elstner and Th. Frauenheim:
Electronic band structure and intermolecular interaction in substituted thiophene polymorphs,
Phys. Rev. B 63, 233204-1 – 233204-4 (2001).
E. Kim, C. Chen, T. Köhler, M. Elstner and Th. Frauenheim:
Theoretical study of a body-centered-tetragonal phase of carbon nitride,
Phys. Rev. B 64, 94107-1 – 94107-6 (2001).
H. Liu, M. Elstner, E. Kaxiras, Th. Frauenheim, J. Hermans and W. Yang:
Quantum mechanics simulation of protein dynamics on long timescale,
Proteins: Structure, Function, and Genetics 44, 484 – 489 (2001).
HOCHSCHULSCHRIFTEN:
Dissertation von Thomas Niehaus: „Entwicklung approximativer Methoden in der zeitabhängigen Dichtefunktionaltheorie“,
Fachbereich Physik, Universität Paderborn, 2001, summa cum laude.
Dissertation von Emadeddin Tajkhorshid: „Molecular modelling study of the biological role of the retinal Schiff base chromophore in bacteriorhodopsin“,
Medizinische Fakultät, Universität Heidelberg, 2001, summa cum laude.
M. Elstner, Th. Frauenheim, E. Kaxiras, G. Seifert and S. Suhai:
A self-consistent charge density-functional based tight-binding scheme for large biomolecules,
Phys. stat. sol. (b) 217, 357-376 (2000).
E. Tajkhorshid, J. Baudry, K. Schulten and S. Suhai:
Molecular dynamics study of the nature and origin of retinal’s twisted structure in bacteriorhodopsin,
Biophys. J. 78, 683-693 (2000).
K. Frimand, H. Bohr, K. J. Jalkanen and S. Suhai:
Structures, vibrational absorption and vibrational circular dichroism spectra of L-alanine in aqueous solution: a density functional theory and RHF study,
Chem. Phys. 255, 165-194 (2000).
Th. Frauenheim, G. Seifert, M. Elstner, Z. Hajnal, G. Jungnickel, D. Porezag, S. Suhai and R. Scholz:
A self-consistent-charge density-functional based tight-binding method for predictive materials simulations in physics, chemistry and biology,
Phys. stat. sol. (b) 217, 41-62 (2000).
I. P. Csonka, B. Paizs, G. Lendvay and S. Suhai:
Proton mobility in protonated peptides: a joint molecular orbital and RRKM study,
Rapid Commun. Mass Spectrom. 14, 417-431 (2000).
B. Paizs, Z. Szlávik, G. Lendvay, K. Vékey and S. Suhai:
Formation of a2+ ions of protonated peptides. An ab initio study,
Rapid Commun. Mass Spectrom. 14, 746-755 (2000).
W.-G. Han, M. Elstner, K. J. Jalkanen, T. Frauenheim and S. Suhai:
Hybrid SCC-DFTB/molecular mechanical studies of H-bonded systems and of N-Acetyl-(L-Ala)n N’-Methylamide helices in water solution,
Int. J. Quant. Chem. 78, 459-479 (2000).
E. Tajkhorshid and S. Suhai:
The dielectric effect of the environment on the pKa of the retinal Schiff base and on the stabilization of the ion pair in bacteriorhodopsin,
J. Mol. Struct. (Theochem) 501-502, 297-313 (2000).
M. Elstner, K. J. Jalkanen, M. Knapp-Mohammady, Th. Frauenheim and S. Suhai:
DFT studies on helix formation in N-acetyl-(L-alanyl)n-N’-methylamide for n=1-20,
Chem. Phys. 256, 15-27 (2000).
I. P. Csonka, B. Paizs and S. Suhai:
Evaluating the formation of salt-bridges. a molecular orbital study,
Chem. Phys. Lett. 326, 129-142, (2000).
O. N. Ventura, M. Kieninger, R. E. Cachau and S. Suhai:
Density functional computational thermochemistry: determination of the enthalpy of formation of sulfine, CH2=S=O, at room temperature,
Chem. Phys. Lett. 329, 145-153 (2000).
B. Paizs, J. Baker, S. Suhai and P. Pulay:
Geometry optimization of large biomolecules in redundant internal coordinates,
J. Chem. Phys. 113, 6566 – 6572 (2000).
S. Suhai, Genomics and Proteomics: Functional and Computational Aspects, Ed.,
Kluwer Academic/Plenum Publishers, New York, 2000.
B. Chevreux, T. Pfisterer and S. Suhai:
Automatic assembly and editing of genomic data,
In “Genomics and Proteomics: Functional and Computational Aspects”, S. Suhai, Ed.,
Kluwer Academic/Plenum Publishers, New York, 2000, pp. 51-65.
B. Mirkin and O. Ritter:
A feature-based approach to discrimination and prediction of protein folding,
In “Genomics and Proteomics: Functional and Computational Aspects”, S. Suhai, Ed.,
Kluwer Academic/Plenum Publishers, New York, 2000, pp. 157-177.
M. Senger, P. Ernst and K.-H. Glatting:
Distributed application management in bioinformatics,
In “Genomics and Proteomics: Functional and Computational Aspects”, S. Suhai, Ed.,
Kluwer Academic/Plenum Publishers, New York, 2000, pp. 215-229.
HOCHSCHULSCHRIFTEN:
Dissertation von Jonathan Karges: „Abstract Resource Language (ARL): Eine Sprache zur Spezifikation und Kontrolle von Biocomputing Experimenten“,
Mathematisch-Naturwissenschaftliche Fakultät, Universität Münster, 2000, cum laude.
Dissertation von Wen-Ge Han: „Ab initio and Hybrid Quantum Mechanical/ Molecular Mechanical (QM/MM) Studies of Biological Systems“,
Medizinische Fakultät, Universität Heidelberg, 2000, cum laude.
E. Tajkhorshid and S. Suhai: Dielectric effects due to the environment on the structure and proton affinity of retinal Schiff base models, Chem. Phys. Lett. 299, 457-464 (1999a).
M. Knapp-Mohammady, K. J. Jalkanen, F. Nardi, R. C. Wade and S. Suhai: L-alanyl-L-alanine in the zwitterionic state: structures determined in the presence of explicit water molecules and with continuum models using density functional theory, Chem. Phys. 240, 63-77 (1999).
E. Tajkhorshid and S. Suhai: The effect of the protein environment on the structure and charge distribution of the retinal Schiff base in bacteriorhodopsin, Theor. Chem. Acc. 101, 180-185 (1999b).
Z. W. Luo and S. Suhai: Estimating linkage disequilibrium between a polymorphic marker locus and a trait locus in natural populations, Genetics 151, 359-371 (1999).
E. Schmid, A. Hotz-Wagenblatt and W. Dröge: Inhibition of the insulin receptor kinase phosphorylation by nitric oxide: Functional and structural aspects, Antioxidants & Redox Signaling 1, 45-53 (1999a).
E. Tajkhorshid, B. Paizs and S. Suhai: Role of isomerization barriers in the pKa control of the retinal Schiff base: A density functional study, Phys. Chem. B 103, 4518-4527 (1999c).
B. Paizs, G. Lendvay, K. Vékey and S. Suhai: Formation of b2+ ions from protonated peptides: an ab initio study, Rapid Commun. Mass Spectrom. 13, 525-533 (1999).
J. L. Sussman, O. Ritter and E. E. Abola: Protein Data Bank, Transactions ACA 32, 7-11 (1999).
W.-G. Han, E. Tajkhorshid and S. Suhai: QM/MM study of the active site of free papain and of the NMA-papain complex, J. Biomol. Structure & Dynamics 16, 1019-1032 (1999).
E. Tajkhorshid and S. Suhai: Influence of the methyl groups on the structure, charge distribution, and proton affinity of the retinal Schiff base, J. Phys. Chem. B 103, 5581-5590 (1999).
P. Hobza, O. Bludsky and S. Suhai: Reliable theoretical treatment of molecular clusters: Counterpoise-corrected potential energy surface and anharmonic vibrational frequencies of the water dimer, Phys. Chem. Chem. Phys. 1, 3073-3078 (1999).
H. G. Bohr, K. J. Jalkanen, M. Elstner, K. Frimand and S. Suhai: A comparative study of MP2, B3LYP, RHF and SCC-DFTB force fields in predicting the vibrational spectra of N-acetyl-L-alanine-N’-methyl amide: VA and VCD spectra, Chem. Phys. 246, 13-36 (1999).
E. Schmid, A. Hotz-Wagenblatt, V. Hack and W. Dröge: Phosphorylation of the insulin receptor kinase by phosphocreatine in combination with hydrogen peroxide: the structural basis of redox priming, FASEB 13, 1491-1500 (1999b).
B. Paizs, E. Tajkhorshid and S. Suhai: Electronic effects on the ground-state rotational barrier of polyene Schiff bases: A molecular orbital study, J. Phys. Chem. B 103, 5388-5395 (1999).
M. Elstner, D. Porezag, G. Seifert, Th. Frauenheim and S. Suhai: Selfconsistent-charge density-functional tight-binding method for simulations of biological molecules, in „Multiscale Modelling of Materials“, Ed. T. Diaz de la Rubia, T. Kaxiras, V. Bulatov, N. M. Ghoniem, R. Phillips, MRS Symp. Proc. 538, 541–546 (1999).
B. Paizs and M. Simonyi: Ring inversion barrier of diazepam and derivatives: An ab initio study, Chirality 11, 651-658 (1999).
J. Grassmann, M. Reczko, S. Suhai and L. Edler: Protein fold class prediction: New methods of statistical classification, Proceedings “Seventh International Conference on Intelligent Systems for Molecular Biology”, T. Lengauer, R. Schneider, P. Bork, D. Brutlag, J. Glasgow, H.-W. Mewes and R. Zimmer, Eds., Heidelberg, 1999, pp. 106-112.