Publications
Work published by The Rohs Lab
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J. Li, T.P. Chiu, and R. Rohs*:
Predicting DNA structure using a deep learning method
Nat. Commun. 15, 1243 (2024)
J.M. Sagendorf, R. Mitra, J. Huang, X.S. Chen, and R. Rohs*:
PNAbind: Structure-based prediction of protein-nucleic acid binding using graph neural networks
bioRxiv 2024.02.27.582387 (2024)
Y. Jiang, T.P. Chiu, R. Mitra, and R. Rohs*:
Probing the role of the protonation state of a minor groove linker histidine in Exd-Hox-DNA binding.
J.A. Weller and R. Rohs*:
DrugHIVE: A deep hierarchical variational autoencoder for the structure-based design of drug-like molecules.
bioRxiv 2023.12.22.573155 (2023)
R. Mitra, J. Li, J.M. Sagendorf, Y. Jiang, T.P. Chiu, and R. Rohs*:
DeepPBS: Geometric deep learning for interpretable prediction of protein-DNA binding specificity.
bioRxiv 2023.12.15.571942 (2023)
J. Li, T.P. Chiu, and R. Rohs*:
Deep DNAshape: Predicting DNA shape considering extended flanking regions using a deep learning method.
bioRxiv 2023.10.22.563383 (2023)
Y. Li, B.H. Cooper, Y. Liu, D. Wu, X. Zhang, R. Rohs, and P.Z. Qin:
CRISPR-Cas9 with truncated 16-nucleotide RNA guides are tuned by target duplex stability beyond the RNA/DNA hybrid.
Biochemistry 62, 2541-2548 (2023)
B.H. Cooper, A.C. Dantas Machado, Y. Gan, O.M. Aparicio, and R. Rohs*:
DNA binding specificity of all four Saccharomyces cerevisiae forkhead transcription factors.
Nucleic Acids Res. 51, 5621-5633 (2023)
Supplementary Information
T.P. Chiu, S. Rao, and R. Rohs*:
Physicochemical models of protein-DNA binding with standard and modified base pairs.
Proc. Natl. Acad. Sci. USA 120, e2205796120 (2023)
Supplementary Information
B.H. Cooper, T.P. Chiu, and R. Rohs*:
Top-Down-Crawl: a method for the ultra-rapid and motif-free alignment of sequences with associated binding metrics.
Bioinformatics 38, 5121-5123 (2022)
Supplementary Information
T.P. Chiu, J. Li, Y. Jiang, and R. Rohs*:
It is in the flanks: Conformational flexibility of transcription factor binding sites.
Biophys. J. 121, 3765-3767 (2022)
E. Oberbeckmann, N. Krietenstein, V. Niebauer, Y. Wang, K. Schall, M. Moldt, T. Straub, R. Rohs, K.-P. Hopfner, P. Korber, and S. Eustermann:
Genome information processing by the INO80 chromatin remodeler positions nucleosomes.
Nat. Commun. 12, 3231 (2021)
Supplementary Information
C.S.K. Lee, M.F. Cheung, J. Li, Y. Zhao, W.H. Lam, V. Ho, R. Rohs, Y. Zhai, D. Leung, and B.-K. Tye:
Humanizing the yeast origin recognition complex.
Nat. Commun. 12, 33 (2021)
Supplementary Information
Y. Le Poul, Y. Xin, L. Ling, B. Mühling, R. Jaenichen, D. Hörl, D. Bunk, H. Harz, H. Leonhardt, Y. Wang, E. Osipova, M. Museridze, D. Dharmadhikari, E. Murphy, R. Rohs, S. Preibisch, B. Prud'homme, and N. Gompel:
Regulatory encoding of quantitative variation in spatial activity of a Drosophila enhancer.
Sci. Adv. 6, eabe2955 (2020)
Supplementary Information
S. Lara-Gonzalez, A.C. Dantas Machado, S. Rao, A.A. Napoli, J. Birktoft, R. Di Felice, R. Rohs*, and C.L. Lawson*:
The RNA polymerase α subunit recognizes the DNA shape of the upstream promoter element.
Biochemistry, 59, 4523-4532 (2020)
Supplementary Information
A.C. Dantas Machado, B.H. Cooper, X. Lei, R. Di Felice, L. Chen, and R. Rohs*:
Landscape of DNA binding signatures of myocyte enhancer factor-2B reveals a unique interplay of base and shape readout.
Nucleic Acids Res. 48, 8529-8544 (2020)
Supplementary Information
Interview of R. Rohs with USC News
X. Lei, J. Zhao, J.M. Sagendorf, N. Rajashekar, J. Xu, A.C. Dantas Machado, C. Sen, R. Rohs, P. Feng, and L. Chen L:
Crystal structures of ternary complexes of MEF2 and NKX2-5 bound to DNA reveal a disease related protein-protein interaction interface.
J. Mol. Biol. 432, 5499-5508 (2020)
Supplementary Information
X. Wu, B. Cao, P. Aquino, T.P. Chiu, C. Chen, S. Jiang, Z. Deng, S. Chen, R. Rohs, L. Wang, J.E. Galagan, and P.C. Dedon:
Epigenetic competition reveals density-dependent regulation and target site plasticity of phosphorothioate epigenetics in bacteria.
Proc. Natl. Acad. Sci. USA 117, 14322-14330 (2020)
Supplementary Information
J.F. Kribelbauer, X.J. Lu, R. Rohs, R.S. Mann, and H.J. Bussemaker:
Towards a mechanistic understanding of DNA methylation readout by transcription factors.
J. Mol. Biol. 432, 1801-1815 (2020)
T.P. Chiu, B. Xin, N. Markarian, Y. Wang, and R. Rohs*:
TFBSshape: an expanded motif database for DNA shape features of transcription factor binding sites.
Nucleic Acids Res. 48, D246-D255 (2020)
Supplementary Information
J.M. Sagendorf, N. Markarian, H.M. Berman, and R. Rohs*:
DNAproDB: an expanded database and web-based tool for structural analysis of DNA-protein complexes.
Nucleic Acids Res. 48, D277-D287 (2020)
Supplementary Information
S. Schwörer, F. Becker, C. Feller, A.H. Baig, U. Köber, H. Henze, J.M. Kraus, B. Xin, A. Lechel, D.B. Lipka, C.S. Varghese, M. Schmidt, R. Rohs, R. Aebersold, K.L. Medina, H. A. Kestler, F. Neri, J. von Maltzahn, S. Tümpel, and K.L. Rudolph:
Author Correction: Epigenetic stress responses induce muscle stem-cell aging by Hoxa9 developmental signals.
Nature 572, E11-E15 (2019)
C. Chu, Z. Li, B. Xin, F. Peng, C. Liu, R. Rohs, Q. Luo, and J. Zhou:
Deep graph embedding for ranking optimization in E-commerce.
Proc. ACM Int. Conf. Inf. Knowl. Manag. 2007-2015 (2018)
X. Wang, T. Zhou*, Z. Wunderlich, M.T. Maurano, A.H. DePace, S.V. Nuzhdin, and R. Rohs*:
Analysis of genetic variation indicates DNA shape involvement in purifying selection.
Mol. Biol. Evol. 35, 1958-1967 (2018)
Supplementary Information
B. Xin and R. Rohs*:
Relationship between histone modifications and transcription factor binding is protein family specific.
Genome Res. 28, 321-333 (2018)
Supplementary Information
S. Rao, T.P. Chiu, J.F. Kribelbauer, R.S. Mann, H.J. Bussemaker*, and R. Rohs*:
Systematic prediction of DNA shape changes due to CpG methylation explains epigenetic effects on protein-DNA binding.
Epigenetics Chromatin 11, 6 (2018)
Supplementary Information
R.Y. Li, R. Di Felice, R. Rohs*, and D.A. Lidar*:
Quantum annealing versus classical machine learning applied to a simplified computational biology problem.
npj Quantum Information 4, 11 (2018)
Supplementary Information
R.N. Azad, D. Zafiropoulos, D. Ober, Y. Jiang, T.P. Chiu, J.M. Sagendorf, R. Rohs*, and T.D. Tullius*:
Experimental maps of DNA structure at nucleotide resolution distinguish intrinsic from protein-induced DNA deformations.
Nucleic Acids Res. 46, 2636-2647 (2018)
Supplementary Information
J. Li, J.M. Sagendorf, T.P. Chiu, M. Pasi, A. Perez, and R. Rohs*:
Expanding the repertoire of DNA shape features for genome-scale studies of transcription factor binding.
Nucleic Acids Res. 45, 12877-12887 (2017)
Supplementary Information
T.P. Chiu, S. Rao, R.S. Mann, B. Honig, and R. Rohs*:
Genome-wide prediction of minor-groove electrostatic potential enables biophysical modeling of protein-DNA binding.
Nucleic Acids Res. 45, 12565-12576 (2017)
Supplementary Information
J. Li, A.C. Dantas Machado, M. Guo, J.M. Sagendorf, Z. Zhou, L. Jiang, X. Chen, D. Wu, L. Qu, Z. Chen, L. Chen*, R. Rohs*, and Y. Chen*:
Structure of the forkhead domain of FOXA2 bound to a complete DNA consensus site.
Biochemistry 56, 3745-3753 (2017)
Supplementary Information
W. Ma, L. Yang, R. Rohs*, and W.S. Noble*:
DNA sequence+shape kernel enables alignment-free modeling of transcription factor binding.
Bioinformatics 33, 3003-3010 (2017)
Supplementary Information
N.S. Tangprasertchai, R. Di Felice, X. Zhang, I.M. Slaymaker, C. Vazquez Reyes, W. Jiang, R. Rohs, and P.Z. Qin:
CRISPR-Cas9 mediated DNA unwinding detected using site-directed spin labeling.
ACS Chem. Biol.12, 1489-1493 (2017)
Supplementary Information
J.M. Sagendorf, H.M. Berman*, and R. Rohs*:
DNAproDB: an interactive tool for structural analysis of DNA-protein complexes.
Nucleic Acids Res. 45, W89-W97 (2017)
Supplementary Information
S. Kasinathan, G.E. Zentner, B. Xin, R. Rohs, and S. Henikoff:
Correspondence: Reply to 'DNA shape is insufficient to explain binding'.
Nat. Commun. 8, 15644 (2017)
RECOMB/ISCB Top-10 Paper in Regulatory and Systems Genomics in 2016/17
L. Yang, Y. Orenstein, A. Jolma, Y. Yin, J. Taipale, R. Shamir*, and R. Rohs*:
Transcription factor family-specific DNA shape readout revealed by quantitative specificity models.
Mol. Syst. Biol. 13, 910 (2017)
Supplementary Information
S. Schwörer, F. Becker, C. Feller, A.H. Baig, U. Köber, H. Henze, J.M. Kraus, B. Xin, A. Lechel, D.B. Lipka, C.S. Varghese, M. Schmidt, R. Rohs, R. Aebersold, K.L. Medina, H. A. Kestler, F. Neri, J. von Maltzahn, S. Tümpel, and K.L. Rudolph:
Epigenetic stress responses induce muscle stem-cell ageing by Hoxa9 developmental signals.
Nature 540, 428-432 (2016)
Supplementary Information
Author Correction
S. Schöne, M. Jurk, M.B. Helabad, I. Dror, I. Lebars, B. Kieffer, P. Imhof, R. Rohs, M. Vingron, M. Thomas-Chollier, and S.H. Meijsing:
Sequences flanking the core-binding site modulate glucocorticoid receptor structure and activity.
Nat. Commun. 7, 12621 (2016)
Supplementary Information
A. Mathelier, B. Xin, T.P. Chiu, L. Yang, R. Rohs*, and W.W. Wasserman*:
DNA shape features improve transcription factor binding site predictions in vivo.
Cell Syst. 3, 278-286 (2016)
Supplementary Information
G. Kuzu, E.G. Kaye, J. Chery, T. Siggers, L. Yang, J.R. Dobson, S. Boor, J. Bliss, W. Liu, G. Jogl, R. Rohs, N.D. Singh, M.L. Bulyk, M.Y. Tolstorukov, and E. Larschan:
Expansion of GA dinucleotide repeats increases the density of CLAMP binding sites on the X-chromosome to promote Drosophila dosage compensation.
PLOS Genet. 12, e1006120 (2016)
Supplementary Information
I. Dror, R. Rohs, and Y. Mandel-Gutfreund:
How motif environment affects transcription factor search dynamics: Finding a needle in a haystack.
BioEssays 38, 605-612 (2016)
T.P. Chiu, F. Comoglio, T. Zhou, L. Yang, R. Paro, and R. Rohs*:
DNAshapeR: an R/Bioconductor package for DNA shape prediction and feature encoding.
Bioinformatics 32, 1211-1213 (2016)
Supplementary Information
G.E. Zentner, S. Kasinathan, B. Xin, R. Rohs, and S. Henikoff:
ChEC-seq kinetics discriminates transcription factor binding sites by DNA sequence and shape in vivo.
Nat. Commun. 6, 8733 (2015)
Supplementary Information
N.S. Tangprasertchai, X. Zhang, Y. Ding, K. Tham, R. Rohs, I.S. Haworth, and P. Z. Qin:
An integrated spin-labeling/computational-modeling approach for mapping global structures of nucleic acids.
Methods Enzymol. 564, 427-453 (2015)
RECOMB/ISCB Top-10 Paper in Regulatory and Systems Genomics in 2015/16
I. Dror, T. Golan, C. Levy, R. Rohs*, and Y. Mandel-Gutfreund*:
A widespread role of the motif environment on transcription factor binding across diverse protein families.
Genome Res. 25, 1268-1280 (2015)
Supplementary Information
Z. Deng, Q. Wang, Z. Liu, M. Zhang, A.C. Dantas Machado, T.P. Chiu, C. Feng, Q. Zhang, L. Yu, L. Qi, J. Zheng, X. Wang, X.M. Huo, X. Qi, X. Li, W. Wu, R. Rohs*, Y. Li*, and Z. Chen*:
Mechanistic insights into metal ion activation and operator recognition by the ferric uptake regulator.
Nat. Commun. 6, 7642 (2015)
Supplementary Information
R. Rohs*, A.C. Dantas Machado, and L. Yang:
Exposing the secrets of sex determination.
Nat. Struct. Mol. Biol. 22, 437-438 (2015)
F. Comoglio, T. Schlumpf, V. Schmid, R. Rohs, C. Beisel, and R. Paro:
High-resolution profiling of Drosophila replication start sites reveals a DNA shape and chromatin signature of metazoan origins.
Cell Rep. 11, 821-834 (2015)
Supplementary Information
RECOMB/ISCB Top-10 Paper in Regulatory and Systems Genomics in 2014/15
N. Abe, I. Dror, L. Yang, M. Slattery, T. Zhou, H.J. Bussemaker, R. Rohs*, and R.S. Mann*:
Deconvolving the recognition of DNA sequence from shape.
Cell 161, 307-318 (2015)
Supplementary Information
M. Levo, E. Zalckvar, E. Sharon, A.C. Dantas Machado, Y. Kalma, M. Lotan-Pompan, A. Weinberger, Z. Yakhini, R. Rohs, and E. Segal:
Unraveling determinants of transcription factor binding outside the core-binding site.
Genome Res. 25, 1018-1029 (2015)
Supplementary Information
RECOMB/ISCB Top-10 Paper in Regulatory and Systems Genomics in 2015/16
T. Zhou˚, N. Shen˚, L. Yang, N. Abe, J. Horton, R.S. Mann, H.J. Bussemaker, R. Gordân*, and R. Rohs*:
Quantitative modeling of transcription factor binding specificities using DNA shape.
Proc. Natl. Acad. Sci. USA 112, 4654-4659 (2015)
Supplementary Information
T. Hadžić, D. Park, K.C. Abruzzi, L. Yang, J.S. Trigg, R. Rohs, M. Rosbash, and P.H. Taghert:
Genome-wide features of neuroendocrine regulation in Drosophila by the basic helix-loop-helix transcription factor DIMMED.
Nucleic Acids Res. 43, 2199-2215 (2015)
Supplementary Information
T.P. Chiu˚, L. Yang˚, T. Zhou, B.J. Main, S.C. Parker, S.V. Nuzhdin, T.D. Tullius, and R. Rohs*:
GBshape: a genome browser database for DNA shape annotations.
Nucleic Acids Res. 43, D103-D109 (2015)
Supplementary Information
A.C. Dantas Machado, T. Zhou, S. Rao, P. Goel, C. Rastogi, A. Lazarovici, H.J. Bussemaker*, and R. Rohs*:
Evolving insights on how cytosine methylation affects protein-DNA binding.
Brief. Funct. Genomics 14, 61-73 (2014)
Feature Review
M. Slattery*, T. Zhou, L. Yang, A.C. Dantas Machado, R. Gordân*, and R. Rohs*:
Absence of a simple code: how transcription factors read the genome.
Trends Biochem. Sci. 39, 381-399 (2014)
RECOMB/ISCB Top-10 Paper in Regulatory and Systems Genomics in 2013/14
I. Barozzi, M. Simonatto, S. Bonifacio, L. Yang, R. Rohs, S. Ghisletti, and G. Natoli:
Coregulation of transcription factor binding and nucleosome occupancy through DNA features of mammalian enhancers.
Mol. Cell 54, 844-857 (2014)
Supplementary Information
X. Zhang, A.C. Dantas Machado, Y. Ding, Y. Chen, Y. Lu, Y. Duan, K.W. Tham, L. Chen, R. Rohs*, and P.Z. Qin*:
Conformations of p53 response elements in solution deduced using site-directed spin labeling and Monte Carlo sampling.
Nucleic Acids Res. 42, 2789-2797 (2014)
Supplementary Information
NAR Breakthrough Article
RECOMB/ISCB Top-10 Paper in Regulatory and Systems Genomics in 2013/14
L. Yang, T. Zhou, I. Dror, A. Mathelier, W.W. Wasserman, R. Gordân, and R. Rohs*:
TFBSshape: a motif database for DNA shape features of transcription factor binding sites.
Nucleic Acids Res. 42, D148-D155 (2014)
Supplementary Information
I. Dror, T. Zhou, Y. Mandel-Gutfreund*, and R. Rohs*:
Covariation between homeodomain transcription factors and the shape of their DNA binding sites.
Nucleic Acids Res. 42, 430-441 (2014)
Supplementary Information
A. Eldar, H. Rozenberg, Y. Diskin-Posner, R. Rohs, and Z. Shakked:
Structural studies of p53 inactivation by DNA-contact mutations and its rescue by suppressor mutations via alternative protein-DNA interactions.
Nucleic Acids Res. 41, 8748-8759 (2013)
Supplementary Information
Y. Chen, X. Zhang, A.C. Dantas Machado, Y. Ding, Z. Chen, P.Z. Qin, R. Rohs, and L. Chen:
Structure of p53 binding to the BAX response element reveals DNA unwinding and compression to accommodate base-pair insertion.
Nucleic Acids Res. 41, 8368-8376 (2013)
Supplementary Information
T. Zhou, L. Yang, Y. Lu, I. Dror, A.C. Dantas Machado, T. Ghane, R. Di Felice, and R. Rohs*:
DNAshape: a method for the high-throughput prediction of DNA structural features on a genome-wide scale.
Nucleic Acids Res. 41, W56-W62 (2013)
Supplementary Information
S.P. Hancock, T. Ghane, D. Cascio, R. Rohs, R. Di Felice, and R.C. Johnson:
Control of minor groove width and Fis protein binding by the purine 2-amino group.
Nucleic Acids Res. 41, 6750-6760 (2013)
Supplementary Information
RECOMB/ISCB Top-10 Paper in Regulatory and Systems Genomics in 2012/13
R. Gordân, N. Shen˚, I. Dror˚, T. Zhou˚, J. Horton, R. Rohs*, and M.L. Bulyk*:
Genomic regions flanking E-box binding sites influence DNA binding specificity of bHLH transcription factors through DNA shape.
Cell Rep. 3, 1093-1104 (2013)
Supplementary Information
RECOMB/ISCB Top-10 Paper in Regulatory and Systems Genomics in 2012/13
A. Lazarovici, T. Zhou˚, A. Shafer˚, A.C. Dantas Machado˚, T. Riley, R. Sandstrom, P.J. Sabo, Y. Lu, R. Rohs*, J.A. Stamatoyannopoulos*, and H.J. Bussemaker*:
Probing DNA shape and methylation state on a genomic scale with DNase I.
Proc. Natl. Acad. Sci. USA 110, 6376-6381 (2013)
Supplementary Information
Y.P. Chang, M. Xu, A.C. Dantas Machado, X.J. Yu, R. Rohs*, and X.S. Chen*:
Mechanism of origin DNA recognition and assembly of an initiator-helicase complex by SV40 large tumor antigen.
Cell Rep. 3, 1117-1127 (2013)
Supplementary Information
A.C. Dantas Machado, S.B. Saleebyan, B.T. Holmes, M. Karelina, J. Tam, S.Y. Kim, K.H. Kim, I. Dror, E. Hodis, E. Martz, P.A. Compeau, and R. Rohs*:
Proteopedia: 3D visualization and annotation of transcription factor-DNA readout modes.
Biochem. Mol. Biol. Educ. 40, 400-401 (2012)
Y. Chen, D.L. Bates, R. Dey, P. Chen, A.C. Dantas Machado, I.A. Laird-Offringa, R. Rohs, and L. Chen:
DNA Binding by GATA Transcription Factor Suggests Mechanisms of DNA Looping and Long-Range Gene Regulation
Cell Rep. 2, 1197-1206 (2012)
Supplementary Information
R. Harris˚, T. Mackoy˚, A.C. Dantas Machado˚, D. Xu, R. Rohs*, and M.O. Fenley*:
Opposites attract: Shape and electrostatic complementarity in protein-DNA complexes
Chapter 3 in T. Schlick, Editor. Innovations in Biomolecular Modeling and Simulation. Volume 2, 53-80 (2012). Biomolecular Sciences Series, Royal Society of Chemistry, RCS Publishing, London, UK.
RECOMB/ISCB Top-10 Paper in Regulatory and Systems Genomics in 2011
M. Slattery, T. Riley, P. Liu, N. Abe, P.Gomez-Alcala, I. Dror, T. Zhou, R. Rohs*, B. Honig*, H.J. Bussemaker*, and R.S. Mann*:
Cofactor binding evokes latent differences in DNA binding specificity between Hox proteins.
Cell 147, 1270-1282 (2011)
Supplementary Information
E.P. Bishop*, R. Rohs*, S.C.J. Parker*, S.M. West, R.S. Mann, B. Honig, and T.D. Tullius:
A map of minor groove shape and electrostatic potential from hydroxyl radical cleavage patterns of DNA
ACS Chem. Biol. 6, 1314-1320 (2011)
Supplementary Information
B. Honig* and R. Rohs*:
Biophysics: Flipping Watson and Crick
Nature 470, 472-473 (2011)
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. 79, 233-269 (2010)
S.M. West, R. Rohs, R.S. Mann, and B. Honig:
Electrostatic interactions between arginines and the minor groove in the nucleosome
J. Biomol. Struct. Dyn. 27, 861–866 (2010)
M. Kitayner˚, H. Rozenberg˚, R. Rohs˚, O. Suad, D. Rabinovich, B. Honig, and Zippora Shakked:
Diversity in DNA recognition by p53 revealed by crystal structures with Hoogsteen base pairs
Nat. Struct. Mol. Biol. 17, 423–429 (2010)
Supplementary Information
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
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
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)
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
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)
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)
*Corresponding author(s)
˚Equal contribution