Browse by Research Team

Article

Solvation oscillations and excited-state dynamics of 2-amino- and 2-hydroxy-7-nitrofluorene and its 2'-deoxyriboside.
Karunakaran, V., Pfaffe, M., Ioffe, I., Senyushkina, T., Kovalenko, S.A., Mahrwald, R., Fartzdinov, V., Sklenar, H. and Ernsting, N.P.
Journal of Physical Chemistry A 112 (18): 4294-4307. 8 May 2008

Using internal and collective variables in Monte Carlo simulations of nucleic acid structures: Chain breakage/closure algorithm and associated Jacobians.
Sklenar, H., Wuestner, D. and Rohs, R.
Journal of Computational Chemistry 27 (3): 309-315. February 2006

Molecular flexibility in ab initio drug docking to DNA: binding-site and binding-mode transitions in all-atom Monte Carlo simulations.
Rohs, R., Bloch, I., Sklenar, H. and Shakked, Z.
Nucleic Acids Research 33 (22): 7048-7057. 13 December 2005

Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. II. Sequence context effects on the dynamical structures of the 10 unique dinucleotide steps.
Dixit, S.B., Beveridge, D.L., Case, D.A., Cheatham, T.E., Guidice, E., Lankas, F., Lavery, R., Maddocks, J.H., Osman, R., Sklenar, H., Thayer, K. and Varnai, P.
Biophysical Journal 89 (6): 3721-3740. December 2005

Improved visualization and quantitative analysis of fluorescent membrane sterol in polarized hepatic cells.
Wuestner, D.
Journal of Microscopy 220 (1): 47-64. 1 October 2005

Structural and energetic origins of sequence-specific DNA bending: Monte Carlo simulations of papillomavirus E2-DNA binding sites.
Rohs, R., Sklenar, H. and Shakked, Z.
Structure with Folding & Design 13 (10): 1499-1509. 1 October 2005

Direct observation of rapid internalization and intracellular transport of sterol by macrophage foam cells.
Wuestner, D., Mondal, M., Tabas, I. and Maxfield, F.R.
Traffic 6 (5): 396-412. 1 January 2005

Mathematical analysis of hepatic high density lipoprotein transport based on quantitative imaging data.
Wuestner, D.
Journal of Biological Chemistry 280 (8): 6766-6779. 1 January 2005

Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides.
Beveridge, D.L., Barreiro, G., Byun, S.K., Case, D.A., Cheatham, T.E., Dixit, S.B., Giudice, E., Lankas, F., Lavery, R., Maddocks, J.H., Osman, R., Seibert, E., Sklenar, H., Stoll, G., Thayer, K.M., Varnai, P. and Young, M.A.
Biophysical Journal 87 (6): 3799-3813. December 2004

Conservation, diversification and expansion of C2H2 zinc finger proteins in the Arabidopsis thaliana genome.
Englbrecht, C.C., Schoof, H. and Boehm, S.
BMC Genomics 5 (1): 39. 5 July 2004

Methylene blue binding to DNA with alternating AT base sequence: minor groove binding is favored over intercalation.
Rohs, R. and Sklenar, H.
Journal of Biomolecular Structure & Dynamics 21 (5): 699-712. 1 April 2004

Different transport routes for high density lipoprotein and its associated free sterol in polarized hepatic cells.
Wuestner, D., Mondal, M., Huang, A. and Maxfield, F.R.
Journal of Lipid Research 45 (3): 427-437. 1 March 2004

Aminophospholipids have no access to the luminal side of the biliary canaliculus - Implications for the specific lipid composition of the bile fluid.
Tannert, A., Wuestner, D., Bechstein, J., Mueller, P., Devaux, P.F. and Herrmann, A.
Journal of Biological Chemistry 278 (42): 40631-40639. 17 October 2003

Genomic expansion and clustering of ZAD-containing C2H2 zinc-finger genes in Drosophila.
Chung, H.R., Schaefer, U., Jaeckle, H. and Boehm, S.
EMBO Reports 3 (12): 1158-1162. 1 December 2002

A standard reference frame for the description of nucleic acid base-pair geometry.
Olson, W.K., Bansal, M., Burley, S.K., Dickerson, R.E., Gerstein, M., Harvey, S.C., Heinemann, U., Lu, X.J., Neidle, S., Shakked, Z., Sklenar, H., Suzuki, M., Tung, C.S., Westhof, E., Wolberger, C. and Berman, H.M.
Journal of Molecular Biology 313 : 229-237. 12 October 2001

Methylene blue binding to DNA with alternating GC base sequence: Continuum treatment of salt effects.
Rohs, R. and Sklenar, H.
Indian Journal of Biochemistry & Biophysics 38 (1-2): 1-6. 1 January 2001

Three novel types of splicing aberrations in the tuberous sclerosis TSC2 gene caused by mutations apart from splice consensus sequences.
Mayer, K., Ballhausen, W., Leistner, W. and Rott, H.D.
Biochimica et Biophysica Acta - Molecular Basis of Disease 1502 (3): 495-507. 15 November 2000

Conformational deformability of RNA: A harmonic mode analysis.
Zacharias, M. and Sklenar, H.
Biophysical Journal 78 (5): 2528-2542. May 2000

Methylene blue binding to DNA with alternating GC base sequence: A modeling study.
Rohs, R., Sklenar, H., Lavery, R. and Roeder, B.
Journal of the American Chemical Society 122 (12): 2860-2866. 29 March 2000

Conformational analysis of single-base bulges in A-form DNA and RNA using a hierarchical approach and energetic evaluation with a continuum solvent model.
Zacharias, M. and Sklenar, H.
Journal of Molecular Biology 289 : 261-275. 4 June 1999

Unraveling proteins: A molecular mechanics study.
Rohs, R., Etchebest, C. and Lavery, R.
Biophysical Journal 76 (5): 2760-2768. May 1999

Harmonic modes as variables to approximately account for receptor flexibility in ligand-receptor docking simulations: application to DNA minor groove ligand complex.
Zacharias, M. and Sklenar, H.
Journal of Computational Chemistry 20 : 287-300. 1 February 1999

Force field based conformational analysis of RNA structural motifs: GNRA tetraloops and their pyrimidine relatives.
Maier, A., Sklenar, H., Kratky, H.F., Renner, A. and Schuster, P.
European Biophysics Journal with Biophysics Letters 28 (7): 564-573. 1999

Nearby stop codons in exons of the neurofibromatosis type 1 gene are disparate splice effectors.
Hoffmeyer, S., Nuernberg, P., Ritter, H., Fahsold, R., Leistner, W., Kaufmann, D. and Krone, W.
American Journal of Human Genetics 62 (2): 269-277. 6 February 1998

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.
Zacharias, M. and Sklenar, H.
Biophysical Journal 73 (6): 2990-3003. December 1997

Komp'iuternyi analiz konformatsionnykh osobennostei DNK TATA-boksov promotorov eukariot. Computer analysis of conformational features of the eukaryotic TATA-box DNA promotors.
Ponomarenko, M.P., Ponomarenko, I.V., Kel', A.E., Kolchanov, N.A., Karas, H., Wingender, E. and Sklenar, H.
Molekuliarnaia Biologiia Moskwa 31 : 733-740. 1 July 1997

Influence of static and dynamic bends on the birefringence decay profile of RNA helices: Brownian dynamics simulations.
Zacharias, M. and Hagerman, P.J.
Biophysical Journal 73 (1): 318-332. July 1997

Variations of the C2H2 zinc finger motif in the yeast genome and classification of yeast zinc finger proteins.
Boehm, S., Frishman, D. and Mewes, H.
Nucleic Acids Research 25 (12): 2464-2469. 15 June 1997

Combining structural analysis of DNA with search routines for the detection of transcription regulatory elements.
Karas, H., Knueppel, R., Schulz, W., Sklenar, H. and Wingender, E.
Computer Applications in the Biosciences 12 : 441-446. 1 January 1997

Computer simulations of X-ray scattering curves: Gelation and crystallization process in amylose solutions.
Mueller, J.J., Gernat, C., Schulz, W., Mueller, E.C., Vorwerg, W. and Damaschun, G.
Biopolymers 35 : 271-288. 1 January 1995

Configurational and rheological properties of cyclic polymers.
Carl, W.
Journal of the Chemical Society-Faraday Transaction 91 (16): 2525-2530. 1 January 1995

Jumna (junction minimisation of nucleic acids).
Lavery, R., Zakrzewska, K. and Sklenar, H.
Computer Physics Communications 91 : 135-158. 1 January 1995

NMR studies and restrained-molecular dynamics calculations of a long A+T-rich stretch in DNA: effects of phosphate charge and solvent approximations.
Leijon, M., Zdunek, J., Fritzsche, H., Sklenar, H. and Graeslund, A.
European Journal of Biochemistry 234 (3): 832-842. 1 January 1995

Perturbation expansion of polymers in shear flow.
Carl, W.
Macromolecular Theory and Simulations 4 : 77-86. 1 January 1995

A simple-model for finitely extensible polymers.
Carl, W.
Macromolecular Theory and Simulations 3 : 705-713. 1 January 1994

The FAR domain defines a new Xenopus laevis zinc finger protein subfamily with specific RNA homopolymer binding activity.
Klocke, B., Koester, M., Hille, S., Bouwmeester, T., Boehm, S., Pieler, T. and Knoechel, W.
Biochimica et Biophysica Acta 1217 : 81-89. 1 January 1994

Conformation of d (GGGATCCC) 2 in crystals and in solution studied by X-ray diffraction, Raman spectroscopy and molecular modelling.
Fabian, H., Hoelzer, W., Heinemann, U., Sklenar, H. and Welfle, H.
Nucleic Acids Research 21 (3): 569-576. 11 February 1993

The structure of the left-handed antiparallel amylose double helix. Theoretical studies.
Schulz, W., Sklenar, H., Hinrichs, W. and Saenger, W.
Biopolymers 33 : 363-375. 1 January 1993

Monte Carlo simulation of the hydration shell of double-helical amylose: a left-handed antiparallel double helix fits best into liquid water structure.
Eisenhaber, F. and Schulz, W.
Biopolymers 32 : 1643-1664. 1 January 1992

Review

Atomistic Monte Carlo simulation of lipid membranes.
Wuestner, D. and Sklenar, H.
International Journal of Molecular Sciences 15 (2): 1767-803. 24 January 2014

Editorial

Protein folding: Solution in sight?
Knapp, E.W. and Sklenar, H.
Journal of Computer Aided Molecular Design 7 : 365-501. 1 January 1993