Peer-Reviewed Publications in Scientific Journals

R. Rohs, X. Jin, S.M. West, R. Joshi, B. Honig, and R.S. Mann: Origins of specificity in protein-DNA recognition Annu. Rev. Biochem. (2010) Invited review, submitted.

R. Rohs*, S.M. West*, A. Sosinky, P. Liu, R.S. Mann, and B. Honig: The role of DNA shape in protein-DNA recognition Nature 461, 1248-1253 (2009) Supplementary Information Nature Editor's summary *Equal contribution. Commentary by T. Tullius: Nature Struct Mol Biol 14, 1118-1119 (2007)

R. Rohs, S.M. West, P. Liu, and B. Honig: Nuance in the double-helix and its role in protein-DNA recognition Curr. Op. Struct. Biol. 19, 171-177 (2009)

R. Joshi, J.M. Passner*, R. Rohs*, R. Jain*, A. Sosinsky*, M.A. Crickmore, V. Jacob, A.K. Aggarwal, B. Honig, and R.S. Mann: Functional specificity of a Hox protein mediated by the recognition of minor groove structure Cell 131, 530-543 (2007) Supplemental Data Cell Leading Edge Section *Equal contribution. Commentary by S.C. Harrison: Nature Struct Mol Biol 14, 1118-1119 (2007)

H. Sklenar, D. Wüstner, and R. Rohs: Using internal and collective variables in Monte Carlo simulations of nucleic acid structures: Chain breakage/closure algorithm and associated Jacobians J. Comput. Chem. 27, 309-315 (2006)

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

R. Rohs*, H. Sklenar, and Z. Shakked: Structural and energetic origins of sequence-specific DNA bending: Monte Carlo simulations of papillomavirus E2-DNA binding sites Structure 13, 1499-1509 (2005) Download Figures 1-7 in high resolution (737 kB) *Corresponding author. Commentary by B. Honig: Structure 13, 1400-1401 (2005)

R. Rohs* and H. Sklenar: Methylene blue binding to DNA with alternating AT base sequence: Minor groove binding is favored over intercalation J. Biomol. Struct. Dyn. 21, 699-711 (2004) *Corresponding author.

R. Rohs and H. Sklenar: Methylene blue binding to DNA with alternating GC base sequence: Continuum treatment of salt effects Indian J. Biochem. Biophys. 38, 1-6 (2001) Invited paper.

R. Rohs, H. Sklenar, R. Lavery, and B. Röder: Methylene blue binding to DNA with alternating GC base sequence: A modeling study J. Am. Chem. Soc. 122, 2860-2866 (2000)

R. Rohs, C. Etchebest, and R. Lavery: Unraveling proteins: A molecular mechanics study Biophys. J. 76, 2760-2768 (1999)

Previews, Reviews and Acknowledgments by other Authors

T. Tullius: Structural biology: DNA binding shapes up. Nature 461, 1225-1226 (2009) Commentary on Rohs et al., Nature 461, 1248-1253 (2009)

S.C. Harrison: Three-dimensional intricacies in protein-DNA recognition and transcriptional control Nature Struct. Mol. Biol. 14, 1118-1119 (2007) Commentary on Joshi, Passner, Rohs et al., Cell 131, 530-543 (2007)

O. Suad, E. Eyal, I. Blumenzweig, N. Kessler, D. Levanon, Y. Groner, and Z. Shakked RUN-CBFβ interaction in C. elegans: Computational prediction and experimental verification J. Biomol. Struct. Dyn. 24, 343-358 (2007) Acknowledges R. Rohs.

C.L. Tang, E. Alexov, A.M. Pyle, and B. Honig: Calculation of pKas in RNA: On the structural origins and functional roles of protonated nucleotides J. Mol. Biol. 366, 1475-1496 (2007) Acknowledges R. Rohs.

T.W. Siggers and B. Honig: Structure-based prediction of C2H2 zinc-finger binding specificity: Sensitivity to docking geometry Nucleic Acids Res. 35, 1085-1097 (2007) Acknowledges R. Rohs.

M. Kitayner, H. Rozenberg, N. Kessler, D. Rabinovich, L. Shaulov, T. Haran, and Z. Shakked: Structural basis of DNA recognition by p53 tetramers Mol. Cell 22, 741-753 (2006) Acknowledges R. Rohs.

T. Siggers, A. Silkov, and B. Honig: Bending in the right direction Structure 13, 1400-1401 (2005) Preview of Rohs et al., Structure 13, 1499-1509 (2005)

I. Agmon, A. Bashan, R. Zarivach, and A. Yonath: Symmetry at the active site of the ribosome: Structural and functional implications Biol. Chem. 386, 833-844 (2005) Acknowledges R. Rohs

Theses and Abstracts Published in Scientific Journals

H. Sklenar and R. Rohs: A new chain breakage/closure algorithm yields fast conformational equilibration of nucleic acid structures in Monte Carlo simulation J. Biomol. Struct. Dyn. 20, 835-836 (2003)

R. Rohs: Simulation of structure formation and ligand binding of nucleic acids in the space of collective and internal variables PhD Thesis, Free University Berlin (2002) Download Statistics

R. Rohs and H. Sklenar: Conformational dynamics of nucleic acids: Monte Carlo sampling in the space of rigid body and sugar pucker variables J. Biomol. Struct. Dyn. 18, 1005-1006 (2001)

R. Rohs and H. Sklenar: Sequence and salt effects on methylene blue binding to DNA with alternating GC and AT base sequences J. Biomol. Struct. Dyn. 18, 938-939 (2001)

R. Rohs: Spektroskopische Untersuchungen und theoretische Modellierungen physikalischer Eigenschaften von Farbstoff-Oligonukleotid-Konjugaten Diploma Thesis, Humboldt University Berlin (1997)