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Wilma K. Olson - Publications

Affiliations: 
Chemistry Rutgers University, New Brunswick, NJ, United States 
Area:
conformation, properties, and interactions of nucleic acids
Website:
http://lifesci.rutgers.edu/~molbiosci/faculty/olson.html

170 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Li S, Olson WK, Lu XJ. Web 3DNA 2.0 for the analysis, visualization, and modeling of 3D nucleic acid structures. Nucleic Acids Research. PMID 31114927 DOI: 10.1093/nar/gkz394  0.44
2019 Olson WK, Li S, Kaukonen T, Colasanti A, Xin Y, Lu XJ. Effects of Noncanonical Base Pairing on RNA Folding: Structural Context and Spatial Arrangements of G∙A Pairs. Biochemistry. PMID 31008589 DOI: 10.1021/acs.biochem.9b00122  0.96
2017 Xu F, Zheng H, Clauvelin N, Lu XJ, Olson WK, Nanda V. Parallels between DNA and collagen - comparing elastic models of the double and triple helix. Scientific Reports. 7: 12802. PMID 29038480 DOI: 10.1038/s41598-017-12878-3  0.56
2016 Perez PJ, Olson WK. Insights into genome architecture deduced from the properties of short Lac repressor-mediated DNA loops. Biophysical Reviews. 8: 135-144. PMID 28510211 DOI: 10.1007/s12551-016-0209-7  0.44
2016 Perez PJ, Olson WK. Insights into Genome Architecture Deduced from the Properties of Short Lac Repressor-mediated DNA Loops. Biophysical Reviews. 8: 135-144. PMID 28133491 DOI: 10.1007/s12551-016-0209-7  0.44
2016 Todolli S, Perez PJ, Clauvelin N, Olson WK. Contributions of Sequence to the Higher-Order Structures of DNA. Biophysical Journal. PMID 27955889 DOI: 10.1016/j.bpj.2016.11.017  0.44
2016 Nizovtseva EV, Clauvelin N, Todolli S, Polikanov YS, Kulaeva OI, Wengrzynek S, Olson WK, Studitsky VM. Nucleosome-free DNA regions differentially affect distant communication in chromatin. Nucleic Acids Research. PMID 27940560 DOI: 10.1093/nar/gkw1240  0.44
2015 Lu XJ, Bussemaker HJ, Olson WK. DSSR: an integrated software tool for dissecting the spatial structure of RNA. Nucleic Acids Research. PMID 26184874 DOI: 10.1093/nar/gkv716  0.44
2015 Clauvelin N, Lo P, Kulaeva OI, Nizovtseva EV, Diaz-Montes J, Zola J, Parashar M, Studitsky VM, Olson WK. Nucleosome positioning and composition modulate in silico chromatin flexibility. Journal of Physics. Condensed Matter : An Institute of Physics Journal. 27: 064112. PMID 25564155 DOI: 10.1088/0953-8984/27/6/064112  0.96
2014 Wei J, Czapla L, Grosner MA, Swigon D, Olson WK. DNA topology confers sequence specificity to nonspecific architectural proteins. Proceedings of the National Academy of Sciences of the United States of America. 111: 16742-7. PMID 25385626 DOI: 10.1073/pnas.1405016111  0.96
2014 Yusufaly TI, Li Y, Singh G, Olson WK. Arginine-phosphate salt bridges between histones and DNA: intermolecular actuators that control nucleosome architecture. The Journal of Chemical Physics. 141: 165102. PMID 25362343 DOI: 10.1063/1.4897978  0.96
2014 Perez PJ, Clauvelin N, Grosner MA, Colasanti AV, Olson WK. What controls DNA looping? International Journal of Molecular Sciences. 15: 15090-108. PMID 25167135 DOI: 10.3390/ijms150915090  0.96
2014 Clauvelin N, Olson WK, Tobias I. Effect of the boundary conditions and influence of the rotational inertia on the vibrational modes of an elastic ring. Journal of Elasticity. 115: 193-224. PMID 24795495 DOI: 10.1007/s10659-013-9453-2  0.96
2013 Yusufaly TI, Li Y, Olson WK. 5-Methylation of cytosine in CG:CG base-pair steps: a physicochemical mechanism for the epigenetic control of DNA nanomechanics. The Journal of Physical Chemistry. B. 117: 16436-42. PMID 24313757 DOI: 10.1021/jp409887t  0.96
2013 Colasanti AV, Grosner MA, Perez PJ, Clauvelin N, Lu XJ, Olson WK. Weak operator binding enhances simulated lac repressor-mediated DNA looping. Biopolymers. 99: 1070-81. PMID 23818216 DOI: 10.1002/bip.22336  0.96
2013 Colasanti AV, Lu XJ, Olson WK. Analyzing and building nucleic acid structures with 3DNA. Journal of Visualized Experiments : Jove. e4401. PMID 23644419 DOI: 10.3791/4401  0.96
2013 Zhurkin VB, Olson WK. Can nucleosomal DNA be described by an elastic model?: comment on "Sequence-dependent collective properties of DNAs and their role in biological systems" by Pasquale De Santis and Anita Scipioni. Physics of Life Reviews. 10: 70-2; discussion 82-. PMID 23587120 DOI: 10.1016/j.plrev.2013.01.009  0.96
2013 Olson WK, Grosner MA, Czapla L, Swigon D. Structural insights into the role of architectural proteins in DNA looping deduced from computer simulations. Biochemical Society Transactions. 41: 559-64. PMID 23514154 DOI: 10.1042/BST20120341  0.96
2013 Czapla L, Grosner MA, Swigon D, Olson WK. Interplay of protein and DNA structure revealed in simulations of the lac operon. Plos One. 8: e56548. PMID 23457581 DOI: 10.1371/journal.pone.0056548  0.96
2012 Clauvelin N, Olson WK, Tobias I. Characterization of the geometry and topology of DNA pictured as a discrete collection of atoms. Journal of Chemical Theory and Computation. 8: 1092-1107. PMID 24791158 DOI: 10.1021/ct200657e  0.96
2012 Olson WK, Clauvelin N, Colasanti AV, Singh G, Zheng G. Insights into Gene Expression and Packaging from Computer Simulations. Biophysical Reviews. 4: 171-178. PMID 23139731 DOI: 10.1007/s12551-012-0093-8  0.96
2012 Wriggers W, Olson WK, Dos Remedios CG. Computational opportunities for remote collaboration and capacity building afforded by Web 2.0 and cloud computing. Biophysical Reviews. 4: 153-160. PMID 23066431 DOI: 10.1007/s12551-012-0085-8  0.96
2012 Mládek A, Sponer JE, Kulhánek P, Lu XJ, Olson WK, Sponer J. Understanding the Sequence Preference of Recurrent RNA Building Blocks using Quantum Chemistry: The Intrastrand RNA Dinucleotide Platform. Journal of Chemical Theory and Computation. 8: 335-347. PMID 22712001 DOI: 10.1021/ct200712b  0.96
2012 Kulaeva OI, Zheng G, Polikanov YS, Colasanti AV, Clauvelin N, Mukhopadhyay S, Sengupta AM, Studitsky VM, Olson WK. Internucleosomal interactions mediated by histone tails allow distant communication in chromatin. The Journal of Biological Chemistry. 287: 20248-57. PMID 22518845 DOI: 10.1074/jbc.M111.333104  0.96
2011 Olson WK, Zhurkin VB. Working the kinks out of nucleosomal DNA. Current Opinion in Structural Biology. 21: 348-57. PMID 21482100 DOI: 10.1016/j.sbi.2011.03.006  0.96
2011 Czapla L, Peters JP, Rueter EM, Olson WK, Maher LJ. Understanding apparent DNA flexibility enhancement by HU and HMGB architectural proteins. Journal of Molecular Biology. 409: 278-89. PMID 21459097 DOI: 10.1016/j.jmb.2011.03.050  0.96
2011 Peckham HE, Olson WK. Nucleic-acid structural deformability deduced from anisotropic displacement parameters. Biopolymers. 95: 254-69. PMID 21280021 DOI: 10.1002/bip.21570  0.96
2010 Xu F, Colasanti AV, Li Y, Olson WK. Long-range effects of histone point mutations on DNA remodeling revealed from computational analyses of SIN-mutant nucleosome structures. Nucleic Acids Research. 38: 6872-82. PMID 20647418 DOI: 10.1093/nar/gkq506  0.96
2010 Xu F, Olson WK. DNA architecture, deformability, and nucleosome positioning. Journal of Biomolecular Structure & Dynamics. 27: 725-39. PMID 20232929 DOI: 10.1080/073911010010524943  0.96
2010 Lu XJ, Olson WK, Bussemaker HJ. The RNA backbone plays a crucial role in mediating the intrinsic stability of the GpU dinucleotide platform and the GpUpA/GpA miniduplex. Nucleic Acids Research. 38: 4868-76. PMID 20223772 DOI: 10.1093/nar/gkq155  0.96
2010 Zheng G, Czapla L, Srinivasan AR, Olson WK. How stiff is DNA? Physical Chemistry Chemical Physics : Pccp. 12: 1399-406. PMID 20119618 DOI: 10.1039/b916183j  0.96
2010 Zheng G, Colasanti AV, Lu XJ, Olson WK. 3DNALandscapes: a database for exploring the conformational features of DNA. Nucleic Acids Research. 38: D267-74. PMID 19906722 DOI: 10.1093/nar/gkp959  0.96
2009 Srinivasan AR, Sauers RR, Fenley MO, Boschitsch AH, Matsumoto A, Colasanti AV, Olson WK. Properties of the Nucleic-acid Bases in Free and Watson-Crick Hydrogen-bonded States: Computational Insights into the Sequence-dependent Features of Double-helical DNA. Biophysical Reviews. 1: 13-20. PMID 21218180 DOI: 10.1007/s12551-008-0003-2  0.96
2009 Britton LA, Olson WK, Tobias I. Two perspectives on the twist of DNA. The Journal of Chemical Physics. 131: 245101. PMID 20059113 DOI: 10.1063/1.3273453  0.96
2009 Zheng G, Lu XJ, Olson WK. Web 3DNA--a web server for the analysis, reconstruction, and visualization of three-dimensional nucleic-acid structures. Nucleic Acids Research. 37: W240-6. PMID 19474339 DOI: 10.1093/nar/gkp358  0.96
2009 Balasubramanian S, Xu F, Olson WK. DNA sequence-directed organization of chromatin: structure-based computational analysis of nucleosome-binding sequences. Biophysical Journal. 96: 2245-60. PMID 19289051 DOI: 10.1016/j.bpj.2008.11.040  0.96
2009 Olson WK, Esguerra M, Xin Y, Lu XJ. New information content in RNA base pairing deduced from quantitative analysis of high-resolution structures. Methods (San Diego, Calif.). 47: 177-86. PMID 19150407 DOI: 10.1016/j.ymeth.2008.12.003  0.96
2009 Xin Y, Olson WK. BPS: a database of RNA base-pair structures. Nucleic Acids Research. 37: D83-8. PMID 18845572 DOI: 10.1093/nar/gkn676  0.96
2008 Swigon D, Olson WK. Mesoscale modeling of multi-protein-DNA assemblies: the role of the catabolic activator protein in Lac-repressor-mediated looping. International Journal of Non-Linear Mechanics. 43: 1082-1093. PMID 23874000 DOI: 10.1016/j.ijnonlinmec.2008.07.003  0.96
2008 Karymov MA, Chinnaraj M, Bogdanov A, Srinivasan AR, Zheng G, Olson WK, Lyubchenko YL. Structure, dynamics, and branch migration of a DNA Holliday junction: a single-molecule fluorescence and modeling study. Biophysical Journal. 95: 4372-83. PMID 18658216 DOI: 10.1529/biophysj.108.135103  0.96
2008 Lu XJ, Olson WK. 3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures. Nature Protocols. 3: 1213-27. PMID 18600227 DOI: 10.1038/nprot.2008.104  0.96
2008 Czapla L, Swigon D, Olson WK. Effects of the nucleoid protein HU on the structure, flexibility, and ring-closure properties of DNA deduced from Monte Carlo simulations. Journal of Molecular Biology. 382: 353-70. PMID 18586040 DOI: 10.1016/j.jmb.2008.05.088  0.96
2008 Tolstorukov MY, Choudhary V, Olson WK, Zhurkin VB, Park PJ. nuScore: a web-interface for nucleosome positioning predictions. Bioinformatics (Oxford, England). 24: 1456-8. PMID 18445607 DOI: 10.1093/bioinformatics/btn212  0.96
2007 Banerjee A, Misra M, Pai D, Shih LY, Woodley R, Lu XJ, Srinivasan AR, Olson WK, Davé RN, Venanzi CA. Feature extraction using molecular planes for fuzzy relational clustering of a flexible dopamine reuptake inhibitor. Journal of Chemical Information and Modeling. 47: 2216-27. PMID 17967005 DOI: 10.1021/ci7001632  0.96
2007 Tolstorukov MY, Colasanti AV, McCandlish DM, Olson WK, Zhurkin VB. A novel roll-and-slide mechanism of DNA folding in chromatin: implications for nucleosome positioning. Journal of Molecular Biology. 371: 725-38. PMID 17585938 DOI: 10.1016/j.jmb.2007.05.048  0.96
2006 Matsumoto A, Olson WK. PREDICTED EFFECTS OF LOCAL CONFORMATIONAL COUPLING AND EXTERNAL RESTRAINTS ON THE TORSIONAL PROPERTIES OF SINGLE DNA MOLECULES. Multiscale Modeling & Simulation : a Siam Interdisciplinary Journal. 5: 1227-1247. PMID 19081755 DOI: 10.1137/060663040  0.96
2006 Swigon D, Coleman BD, Olson WK. Modeling the Lac repressor-operator assembly: the influence of DNA looping on Lac repressor conformation. Proceedings of the National Academy of Sciences of the United States of America. 103: 9879-84. PMID 16785444 DOI: 10.1073/pnas.0603557103  0.96
2006 Czapla L, Swigon D, Olson WK. Sequence-dependent effects in the cyclization of short DNA Journal of Chemical Theory and Computation. 2: 685-695. DOI: 10.1021/ct060025+  0.96
2006 Olson WK, Colasanti AV, Li Y, Ge W, Zheng G, Zhurkin VB. DNA simulation benchmarks as revealed by X-ray structures Computational Studies of Rna and Dna. 235-257. DOI: 10.1007/978-1-4020-4851-3_9  0.96
2005 Liu G, Geurts AM, Yae K, Srinivasan AR, Fahrenkrug SC, Largaespada DA, Takeda J, Horie K, Olson WK, Hackett PB. Target-site preferences of Sleeping Beauty transposons. Journal of Molecular Biology. 346: 161-73. PMID 15663935 DOI: 10.1016/j.jmb.2004.09.086  0.96
2005 Ge W, Schneider B, Olson WK. Knowledge-based elastic potentials for docking drugs or proteins with nucleic acids. Biophysical Journal. 88: 1166-90. PMID 15501936 DOI: 10.1529/biophysj.104.043612  0.96
2005 Matsumoto A, Tobias I, Olson WK. Normal-mode analysis of circular DNA at the base-pair level. 1. Comparison of computed motions with the predicted behavior of an ideal elastic rod Journal of Chemical Theory and Computation. 1: 117-129. DOI: 10.1021/ct049950r  0.96
2005 Matsumoto A, Tobias I, Olson WK. Normal-mode analysis of circular DNA at the base-pair level. 2. Large-scale configurational transformation of a naturally curved molecule Journal of Chemical Theory and Computation. 1: 130-142. DOI: 10.1021/ct049949s  0.96
2004 Olson WK, Swigon D, Coleman BD. Implications of the dependence of the elastic properties of DNA on nucleotide sequence. Philosophical Transactions. Series a, Mathematical, Physical, and Engineering Sciences. 362: 1403-22. PMID 15306458 DOI: 10.1098/rsta.2004.1380  0.96
2003 Lu XJ, Olson WK. 3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures. Nucleic Acids Research. 31: 5108-21. PMID 12930962 DOI: 10.1093/nar/gkg680  0.96
2003 Coleman BD, Olson WK, Swigon D. Theory of sequence-dependent DNA elasticity Journal of Chemical Physics. 118: 7127-7140. DOI: 10.1063/1.1559690  0.96
2002 Wang L, Hingerty BE, Srinivasan AR, Olson WK, Broyde S. Accurate representation of B-DNA double helical structure with implicit solvent and counterions. Biophysical Journal. 83: 382-406. PMID 12080128 DOI: 10.1016/S0006-3495(02)75177-1  0.96
2002 Matsumoto A, Olson WK. Sequence-dependent motions of DNA: a normal mode analysis at the base-pair level. Biophysical Journal. 83: 22-41. PMID 12080098 DOI: 10.1016/S0006-3495(02)75147-3  0.96
2002 Kosikov KM, Gorin AA, Lu XJ, Olson WK, Manning GS. Bending of DNA by asymmetric charge neutralization: all-atom energy simulations. Journal of the American Chemical Society. 124: 4838-47. PMID 11971734 DOI: 10.1021/ja0125218  0.96
2001 Olson WK, Bansal M, Burley SK, Dickerson RE, Gerstein M, Harvey SC, Heinemann U, Lu XJ, Neidle S, Shakked Z, Sklenar H, Suzuki M, Tung CS, Westhof E, Wolberger C, et al. A standard reference frame for the description of nucleic acid base-pair geometry. Journal of Molecular Biology. 313: 229-37. PMID 11601858 DOI: 10.1006/jmbi.2001.4987  0.96
2001 Ruan Q, Zhuang P, Li S, Perlow R, Srinivasan AR, Lu XJ, Broyde S, Olson WK, Geacintov NE. Base sequence effects in bending induced by bulky carcinogen-DNA adducts: experimental and computational analysis. Biochemistry. 40: 10458-72. PMID 11523987 DOI: 10.1021/bi002643x  0.96
2000 Katritch V, Olson WK, Vologodskii A, Dubochet J, Stasiak A. Tightness of random knotting. Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics. 61: 5545-9. PMID 11031608  0.96
2000 Lu XJ, Shakked Z, Olson WK. A-form conformational motifs in ligand-bound DNA structures. Journal of Molecular Biology. 300: 819-40. PMID 10891271 DOI: 10.1006/jmbi.2000.3690  0.96
2000 Li TK, Bathory E, LaVoie EJ, Srinivasan AR, Olson WK, Sauers RR, Liu LF, Pilch DS. Human topoisomerase I poisoning by protoberberines: potential roles for both drug-DNA and drug-enzyme interactions. Biochemistry. 39: 7107-16. PMID 10852708 DOI: 10.1021/bi000171g  0.96
2000 Olson WK, Zhurkin VB. Modeling DNA deformations. Current Opinion in Structural Biology. 10: 286-97. PMID 10851199 DOI: 10.1016/S0959-440X(00)00086-5  0.96
2000 Jin E, Katritch V, Olson WK, Kharatisvili M, Abagyan R, Pilch DS. Aminoglycoside binding in the major groove of duplex RNA: the thermodynamic and electrostatic forces that govern recognition. Journal of Molecular Biology. 298: 95-110. PMID 10756107 DOI: 10.1006/jmbi.2000.3639  0.96
2000 Benevides JM, Li T, Lu XJ, Srinivasan AR, Olson WK, Weiss MA, Thomas GJ. Protein-directed DNA structure II. Raman spectroscopy of a leucine zipper bZIP complex. Biochemistry. 39: 548-56. PMID 10642179 DOI: 10.1021/bi990053x  0.96
2000 Benevides JM, Chan G, Lu XJ, Olson WK, Weiss MA, Thomas GJ. Protein-directed DNA structure. I. Raman spectroscopy of a high-mobility-group box with application to human sex reversal. Biochemistry. 39: 537-47. PMID 10642178 DOI: 10.1021/bi9900525  0.96
2000 Katritch V, Bustamante C, Olson WK. Pulling chromatin fibers: computer simulations of direct physical micromanipulations. Journal of Molecular Biology. 295: 29-40. PMID 10623506 DOI: 10.1006/jmbi.1999.3021  0.96
2000 Fenley MO, Olson WK, Manning GS. Dependence of counterion binding on DNA shape as determined by counterion condensation theory Macromolecules. 33: 1899-1903. DOI: 10.1021/ma990191u  0.96
1999 Chalikian TV, Völker J, Srinivasan AR, Olson WK, Breslauer KJ. The hydration of nucleic acid duplexes as assessed by a combination of volumetric and structural techniques. Biopolymers. 50: 459-71. PMID 10479730 DOI: 10.1002/(SICI)1097-0282(19991015)50:5<459::AID-BIP1>3.0.CO;2-B  0.96
1999 Martino JA, Katritch V, Olson WK. Influence of nucleosome structure on the three-dimensional folding of idealized minichromosomes. Structure (London, England : 1993). 7: 1009-22. PMID 10467141 DOI: 10.1016/S0969-2126(99)80127-0  0.96
1999 Kosikov KM, Gorin AA, Zhurkin VB, Olson WK. DNA stretching and compression: large-scale simulations of double helical structures. Journal of Molecular Biology. 289: 1301-26. PMID 10373369 DOI: 10.1006/jmbi.1999.2798  0.96
1999 Lu XJ, Babcock MS, Olson WK. Overview of nucleic acid analysis programs. Journal of Biomolecular Structure & Dynamics. 16: 833-43. PMID 10217453 DOI: 10.1080/07391102.1999.10508296  0.96
1999 Lu XJ, Olson WK. Resolving the discrepancies among nucleic acid conformational analyses. Journal of Molecular Biology. 285: 1563-75. PMID 9917397 DOI: 10.1006/jmbi.1998.2390  0.96
1999 Boschitsch AH, Fenley MO, Olson WK. A Fast Adaptive Multipole Algorithm for Calculating Screened Coulomb (Yukawa) Interactions Journal of Computational Physics. 151: 212-241. DOI: 10.1006/jcph.1998.6176  0.96
1998 Fenley MO, Manning GS, Marky NL, Olson WK. Excess counterion binding and ionic stability of kinked and branched DNA. Biophysical Chemistry. 74: 135-52. PMID 9760723 DOI: 10.1016/S0301-4622(98)00171-9  0.96
1998 Olson WK, Gorin AA, Lu XJ, Hock LM, Zhurkin VB. DNA sequence-dependent deformability deduced from protein-DNA crystal complexes. Proceedings of the National Academy of Sciences of the United States of America. 95: 11163-8. PMID 9736707 DOI: 10.1073/pnas.95.19.11163  0.96
1998 Martino JA, Olson WK. Modeling chain folding in protein-constrained circular DNA. Biophysical Journal. 74: 2491-500. PMID 9591675 DOI: 10.1016/S0006-3495(98)77957-3  0.96
1998 Srinivasan AR, Olson WK. Molecular models of nucleic acid triple helixes. II. PNA and 2'-5' backbone complexes Journal of the American Chemical Society. 120: 492-499. DOI: 10.1021/ja972721c  0.96
1998 Srinivasan AR, Olson WK. Molecular models of nucleic acid triple helixes. I. DNA and RNA backbone complexes Journal of the American Chemical Society. 120: 484-491. DOI: 10.1021/ja972720k  0.96
1997 Pilch DS, Yu C, Makhey D, LaVoie EJ, Srinivasan AR, Olson WK, Sauers RR, Breslauer KJ, Geacintov NE, Liu LF. Minor groove-directed and intercalative ligand-DNA interactions in the poisoning of human DNA topoisomerase I by protoberberine analogs. Biochemistry. 36: 12542-53. PMID 9376359 DOI: 10.1021/bi971272q  0.96
1997 Liu G, Schlick T, Olson AJ, Olson WK. Configurational transitions in Fourier series-represented DNA supercoils. Biophysical Journal. 73: 1742-62. PMID 9336170 DOI: 10.1016/S0006-3495(97)78205-5  0.96
1997 Xu Z, Pilch DS, Srinivasan AR, Olson WK, Geacintov NE, Breslauer KJ. Modulation of nucleic acid structure by ligand binding: induction of a DNA.RNA.DNA hybrid triplex by DAPI intercalation. Bioorganic & Medicinal Chemistry. 5: 1137-47. PMID 9222508 DOI: 10.1016/S0968-0896(97)00050-3  0.96
1997 Katritch V, Olson WK, Pieranski P, Dubochet J, Stasiak A. Properties of ideal composite knots. Nature. 388: 148-51. PMID 9217153 DOI: 10.1038/40582  0.96
1997 Martino JA, Olson WK. Modeling protein-induced configurational changes in DNA minicircles. Biopolymers. 41: 419-30. PMID 9080777 DOI: 10.1002/(SICI)1097-0282(19970405)41:4<419::AID-BIP6>3.0.CO;2-P  0.96
1997 Westcott TP, Tobias I, Olson WK. Modeling self-contact forces in the elastic theory of DNA supercoiling Journal of Chemical Physics. 107: 3967-3980.  0.96
1996 Langowski J, Olson WK, Pedersen SC, Tobias I, Westcott TP, Yang Y. DNA supercoiling, localized bending and thermal fluctuations. Trends in Biochemical Sciences. 21: 50. PMID 8851658 DOI: 10.1016/0968-0004(96)80863-2  0.96
1996 Olson WK. Simulating DNA at low resolution. Current Opinion in Structural Biology. 6: 242-56. PMID 8728659 DOI: 10.1016/S0959-440X(96)80082-0  0.96
1996 Gelbin A, Schneider B, Clowney L, Hsieh SH, Olson WK, Berman HM. Geometric parameters in nucleic acids: Sugar and phosphate constituents Journal of the American Chemical Society. 118: 519-529. DOI: 10.1021/ja9528846  0.96
1996 Clowney L, Jain SC, Srinivasan AR, Westbrook J, Olson WK, Berman HM. Geometric parameters in nucleic acids: Nitrogenous bases Journal of the American Chemical Society. 118: 509-518. DOI: 10.1021/ja952883d  0.96
1996 Fenley MO, Olson WK, Chua K, Boschitsch AH. Fast adaptive multipole method for computation of electrostatic energy in simulations of polyelectrolyte DNA Journal of Computational Chemistry. 17: 976-991.  0.96
1995 Gorin AA, Zhurkin VB, Olson WK. B-DNA twisting correlates with base-pair morphology. Journal of Molecular Biology. 247: 34-48. PMID 7897660 DOI: 10.1006/jmbi.1994.0120  0.96
1995 Yang Y, Westcott TP, Pedersen SC, Tobias I, Olson WK. Effects of localized bending on DNA supercoiling. Trends in Biochemical Sciences. 20: 313-9. PMID 7667890 DOI: 10.1016/S0968-0004(00)89058-1  0.96
1995 Olson WK, Babcock MS, Gorin A, Liu G, Marky NL, Martino JA, Pedersen SC, Srinivasan AR, Tobias I, Westcott TP. Flexing and folding double helical DNA. Biophysical Chemistry. 55: 7-29. PMID 7632878 DOI: 10.1016/0301-4622(94)00139-B  0.96
1995 Westcott TP, Tobias I, Olson WK. Elasticity theory and numerical analysis of DNA supercoiling: An application to DNA looping Journal of Physical Chemistry. 99: 17926-17935.  0.96
1994 Babcock MS, Olson WK. The effect of mathematics and coordinate system on comparability and "dependencies" of nucleic acid structure parameters. Journal of Molecular Biology. 237: 98-124. PMID 8133524 DOI: 10.1006/jmbi.1994.1212  0.96
1994 Babcock MS, Pednault EP, Olson WK. Nucleic acid structure analysis. Mathematics for local Cartesian and helical structure parameters that are truly comparable between structures. Journal of Molecular Biology. 237: 125-56. PMID 8133513 DOI: 10.1006/jmbi.1994.1213  0.96
1994 Marky NL, Olson WK. Spatial translational motions of base pairs in DNA molecules: application of the extended matrix generator method. Biopolymers. 34: 121-42. PMID 8110965 DOI: 10.1002/bip.360340113  0.96
1994 Marky NL, Olson WK. Configurational statistics of the DNA duplex: extended generator matrices to treat the rotations and translations of adjacent residues. Biopolymers. 34: 109-20. PMID 8110963 DOI: 10.1002/bip.360340112  0.96
1994 Zhang P, Tobias I, Olson WK. Computer simulation of protein-induced structural changes in closed circular DNA. Journal of Molecular Biology. 242: 271-90. PMID 8089847 DOI: 10.1006/jmbi.1994.1578  0.96
1994 Srinivasan AR, Olson WK. Computer models of DNA four-way junctions. Biochemistry. 33: 9389-404. PMID 8068615  0.96
1994 Fenley MO, Olson WK, Tobias I, Manning GS. Electrostatic effects in short superhelical DNA. Biophysical Chemistry. 50: 255-71. PMID 8011947 DOI: 10.1016/0301-4622(93)E0094-L  0.96
1994 Schlick T, Olson WK, Westcott T, Greenberg JP. On higher buckling transitions in supercoiled DNA. Biopolymers. 34: 565-97. PMID 8003619 DOI: 10.1002/bip.360340502  0.96
1994 Schlick T, Li B, Olson WK. The influence of salt on the structure and energetics of supercoiled DNA. Biophysical Journal. 67: 2146-66. PMID 7696459 DOI: 10.1016/S0006-3495(94)80732-5  0.96
1994 Tobias I, Coleman BD, Olson WK. The dependence of DNA tertiary structure on end conditions: Theory and implications for topological transitions The Journal of Chemical Physics. 101: 10990-10996.  0.96
1993 Goldman C, Olson WK. DNA denaturation as a problem of translational-symmetry restoration. Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics. 48: 1461-1468. PMID 9960735 DOI: 10.1103/PhysRevE.48.1461  0.96
1993 Tobias I, Olson WK. The effect of intrinsic curvature on supercoiling: predictions of elasticity theory. Biopolymers. 33: 639-46. PMID 8467069 DOI: 10.1002/bip.360330413  0.96
1993 Erie DA, Breslauer KJ, Olson WK. A Monte Carlo method for generating structures of short single-stranded DNA sequences. Biopolymers. 33: 75-105. PMID 8427940 DOI: 10.1002/bip.360330109  0.96
1993 Erie DA, Suri AK, Breslauer KJ, Jones RA, Olson WK. Theoretical predictions of DNA hairpin loop conformations: correlations with thermodynamic and spectroscopic data. Biochemistry. 32: 436-54. PMID 8422353  0.96
1993 Olson WK, Marky NL, Jernigan RL, Zhurkin VB. Influence of fluctuations on DNA curvature. A comparison of flexible and static wedge models of intrinsically bent DNA. Journal of Molecular Biology. 232: 530-54. PMID 8345522 DOI: 10.1006/jmbi.1993.1409  0.96
1993 Schneider B, Cohen DM, Schleifer L, Srinivasan AR, Olson WK, Berman HM. A systematic method for studying the spatial distribution of water molecules around nucleic acid bases. Biophysical Journal. 65: 2291-303. PMID 8312469 DOI: 10.1016/S0006-3495(93)81306-7  0.96
1993 Jin R, Chapman WH, Srinivasan AR, Olson WK, Breslow R, Breslauer KJ. Comparative spectroscopic, calorimetric, and computational studies of nucleic acid complexes with 2',5"-versus 3',5"-phosphodiester linkages. Proceedings of the National Academy of Sciences of the United States of America. 90: 10568-72. PMID 8248146 DOI: 10.1073/pnas.90.22.10568  0.96
1993 Babcock MS, Pednault EP, Olson WK. Nucleic acid structure analysis: a users guide to a collection of new analysis programs. Journal of Biomolecular Structure & Dynamics. 11: 597-628. PMID 7510497 DOI: 10.1080/07391102.1993.10508018  0.96
1993 Olson WK. Appendix: Limiting Chain Dimensions and Persistence Length of Idealized DNA Journal of Molecular Biology. 232: 552-554. DOI: 10.1006/jmbi.1993.1410  0.96
1993 Yang Y, Tobias I, Olson WK. Finite element analysis of DNA supercoiling The Journal of Chemical Physics. 98: 1673-1686.  0.96
1992 Srinivasan AR, Olson WK. DNA associations: packing calculations in A-, B-, and Z-DNA structures. Biophysical Chemistry. 43: 279-310. PMID 1643240 DOI: 10.1016/0301-4622(92)85027-2  0.96
1992 Schlick T, Olson WK. Supercoiled DNA energetics and dynamics by computer simulation. Journal of Molecular Biology. 223: 1089-119. PMID 1538391 DOI: 10.1016/0022-2836(92)90263-J  0.96
1992 Schlick T, Olson WK. Trefoil knotting revealed by molecular dynamics simulations of supercoiled DNA. Science (New York, N.Y.). 257: 1110-5. PMID 1509261  0.96
1992 Berman HM, Olson WK, Beveridge DL, Westbrook J, Gelbin A, Demeny T, Hsieh SH, Srinivasan AR, Schneider B. The nucleic acid database. A comprehensive relational database of three-dimensional structures of nucleic acids. Biophysical Journal. 63: 751-9. PMID 1384741 DOI: 10.1016/S0006-3495(92)81649-1  0.96
1992 Srinivasan AR, Westbrook JD, Olson WK. An interactive FORTRAN program for three-dimensional molecular visualization Computers and Chemistry. 16: 265-266. DOI: 10.1016/0097-8485(92)80013-P  0.96
1992 Fenley MO, Manning GS, Olson WK. Electrostatic persistence length of a smoothly bending polyion computed by numerical counterion condensation theory Journal of Physical Chemistry. 96: 3963-3969.  0.96
1991 Olson WK, Zhang PS. Computer simulation of DNA supercoiling. Methods in Enzymology. 203: 403-32. PMID 1762565  0.96
1991 Weller DD, Daly DT, Olson WK, Summerton JE. Molecular modeling of acyclic polyamide oligonucleotide analogues Journal of Organic Chemistry. 56: 6000-6006.  0.96
1990 Fenley MO, Manning GS, Olson WK. A numerical counterion condensation analysis of the B-Z transition of DNA. Biopolymers. 30: 1205-13. PMID 2085658 DOI: 10.1002/bip.360301306  0.96
1990 Fenley MO, Manning GS, Olson WK. Approach to the limit of counterion condensation. Biopolymers. 30: 1191-203. PMID 2085657 DOI: 10.1002/bip.360301305  0.96
1989 Hao MH, Olson WK. Modeling DNA supercoils and knots with B-spline functions. Biopolymers. 28: 873-900. PMID 2720128 DOI: 10.1002/bip.360280407  0.96
1989 Erie DA, Jones RA, Olson WK, Sinha NK, Breslauer KJ. Melting behavior of a covalently closed, single-stranded, circular DNA. Biochemistry. 28: 268-73. PMID 2706250  0.96
1989 Hao MH, Olson WK. Molecular modeling and energy refinement of supercoiled DNA. Journal of Biomolecular Structure & Dynamics. 7: 661-92. PMID 2627304 DOI: 10.1080/07391102.1989.10508513  0.96
1989 Hao MH, Olson WK. Global equilibrium configurations of supercoiled DNA Macromolecules. 22: 3292-3303.  0.96
1989 Srinivasan AR, Olson WK. Viewing stereo drawings Journal of Chemical Education. 66: 664-665.  0.96
1988 Olson WK, Srinivasan AR. The translation of DNA primary base sequence into three-dimensional structure. Computer Applications in the Biosciences : Cabios. 4: 133-42. PMID 3382987  0.96
1988 Maroun RC, Olson WK. Base sequence effects in double-helical DNA. III. Average properties of curved DNA. Biopolymers. 27: 585-603. PMID 3370295 DOI: 10.1002/bip.360270404  0.96
1988 Maroun RC, Olson WK. Base sequence effects in double-helical DNA. II. Configurational statistics of rodlike chains. Biopolymers. 27: 561-84. PMID 3370294 DOI: 10.1002/bip.360270403  0.96
1988 Srinivasan AR, Olson WK. Spatial density distributions for illustrating the base sequence dependent features of double helical DNA: Computer graphic visualization of Monte Carlo chain simulations Journal of Molecular Graphics. 6: 126-134. DOI: 10.1016/0263-7855(88)80064-X  0.96
1988 Srinivasan AR, Olson WK. Colour illustrations Journal of Molecular Graphics. 6: 141-147.  0.96
1987 Marky NL, Olson WK. Loop formation in polynucleotide chains. II. Flexibility of the anticodon loop of tRNAPhe. Biopolymers. 26: 415-38. PMID 3646072 DOI: 10.1002/bip.360260309  0.96
1987 Srinivasan AR, Torres R, Clark W, Olson WK. Base sequence effects in double helical DNA. I. Potential energy estimates of local base morphology. Journal of Biomolecular Structure & Dynamics. 5: 459-96. PMID 3271482 DOI: 10.1080/07391102.1987.10506409  0.96
1987 Srinivasan AR, Olson WK. Nucleic acid model building: the multiple backbone solutions associated with a given base morphology. Journal of Biomolecular Structure & Dynamics. 4: 895-938. PMID 3270539 DOI: 10.1080/07391102.1987.10507690  0.96
1986 Olson WK, Cicariello J. Computer simulation of DNA supercoiling. Annals of the New York Academy of Sciences. 482: 69-81. PMID 3471115  0.96
1986 Srinivasan AR, Olson WK. Conformational studies of (2'-5') polynucleotides: theoretical computations of energy, base morphology, helical structure, and duplex formation. Nucleic Acids Research. 14: 5461-79. PMID 2426656  0.36
1986 Srinivasan AR, Olson WK. Conformational studies of (2′-5′) polynucleotides: Theorotical computations of energy, base morphology helical structure, and duplex formation Nucleic Acids Research. 14: 5461-5479. DOI: 10.1093/nar/14.13.5461  0.96
1985 Olson WK, Marky NL, Srinivasan AR, Do KD, Cicariello J. Theoretical studies of perturbed nucleic acid structures. Progress in Clinical and Biological Research. 172: 109-21. PMID 3991667  0.96
1984 Levy RM, Srinivasan AR, Olson WK, McCammon JA. Quasi-harmonic method for studying very low frequency modes in proteins. Biopolymers. 23: 1099-112. PMID 6733249 DOI: 10.1002/bip.360230610  0.96
1983 Taylor ER, Olson WK. Theoretical studies of nucleic acid interactions. I. Estimates of conformational mobility in intercalated chains. Biopolymers. 22: 2667-702. PMID 6667335 DOI: 10.1002/bip.360221213  0.96
1983 Olson WK, Srinivasan AR, Marky NL, Balaji VN. Theoretical probes of DNA conformation examining the B leads to Z conformational transition. Cold Spring Harbor Symposia On Quantitative Biology. 47: 229-41. PMID 6574843  0.96
1982 Hingerty BE, Broyde SB, Olson WK. The poly(rU) coil: a minimum-energy model that matches experimental observations. Biopolymers. 21: 1167-88. PMID 6178444 DOI: 10.1002/bip.360210612  0.96
1982 Olson WK. Computational studies of polynucleotide flexibility Nucleic Acids Research. 10: 777-787. DOI: 10.1093/nar/10.3.777  0.96
1982 Marky NL, Olson WK. Loop formation in polynucleotide chains. I. Theory of hairpin loop closure Biopolymers. 21: 2329-2344.  0.96
1982 Olson WK, Sussman JL. How flexible is the furanose ring? 1. A comparison of experimental and theoretical studies Journal of the American Chemical Society. 104: 270-278.  0.96
1982 Olson WK. How flexible is the furanose ring? 2. An updated potential energy estimate Journal of the American Chemical Society. 104: 278-286.  0.96
1981 Olson WK. Three-state models of furanose pseudorotation Nucleic Acids Research. 9: 1251-1262. DOI: 10.1093/nar/9.5.1251  0.96
1980 Srinivasan AR, Olson WK. Yeast tRNA(Phe) conformation wheels: A novel probe of the monoclinic and orthorhombic models Nucleic Acids Research. 8: 2307-2329. PMID 7001355  0.96
1980 Srinivasan AR, Olson WK. Protein conformation wheels: cytochromes and lysozymes International Journal of Peptide and Protein Research. 16: 111-123. PMID 6257619  0.96
1980 Olson WK. Configurational statistics of polynucleotide chains. An updated virtual bond model to treat effects of base stacking Macromolecules. 13: 721-728.  0.96
1979 Olson WK. The flexible DNA double helix. II. Superhelix formation Biopolymers - Peptide Science Section. 18: 1235-1260. PMID 435614  0.96
1979 Olson WK. The flexible DNA double helix. I. Average dimensions and distribution functions Biopolymers - Peptide Science Section. 18: 1213-1233. PMID 435613  0.96
1978 Olson WK. Spatial configuration of ordered polynucleotide chains. V. Conformational energy estimates of helical structure Biopolymers. 17: 1015-1040.  0.96
1977 Olson WK. Spatial configuration of ordered polynucleotide chains: a new novel double helix Proceedings of the National Academy of Sciences of the United States of America. 74: 1775-1779. PMID 266701  0.96
1976 Olson WK. The spatial configuration of ordered polynucleotide chains. I. Helix formation and base stacking Biopolymers. 15: 859-878. PMID 1260107  0.96
1976 Olson WK, Manning GS. A configurational interpretation of the axial phosphate spacing in polynucleotide helices and random coils Biopolymers. 15: 2391-2405. PMID 1000049  0.96
1976 Olson WK, Dasika RD. Spatial configuration of ordered polynucleotide chains. 3. Polycyclonucleotides Journal of the American Chemical Society. 98: 5371-5380. PMID 956562  0.96
1975 Olson WK. Configurational statistics of polynucleotide chains. A single virtual bond treatment Macromolecules. 8: 272-275. PMID 1152526  0.96
1975 Olson WK. The spatial configuration of ordered polynucleotide chains. II. The poly(rA) helix Nucleic Acids Research. 2: 2055-2068. PMID 1052529  0.96
1975 Olson WK. Configuration dependent properties of randomly coiling polynucleotide chains. I. A comparison of theoretical energy estimates Biopolymers. 14: 1775-1795.  0.96
1975 Olson WK. Configuration dependent properties of randomly coiling polynucleotide chains. II. The role of the phosphodiester linkage Biopolymers. 14: 1797-1810.  0.96
1973 Olson WK. Syn Anti effects on the spatial configuration of polynucleotide chains Biopolymers. 12: 1787-1814. PMID 4733709  0.96
1972 Olson WK, Flory PJ. Spatial configurations of polynucleotide chains. 3. Polydeoxyribonucleotides. Biopolymers. 11: 57-66. PMID 5008185 DOI: 10.1002/bip.1972.360110104  0.96
1972 Olson WK, Flory PJ. Spatial configurations of polynucleotide chains. I. Steric interactions in polyribonucleotides: a virtual bond model. Biopolymers. 11: 1-23. PMID 5008180 DOI: 10.1002/bip.1972.360110102  0.96
1972 Olson WK, Flory PJ. Spatial configuration of polynucleotide chains. II. Conformational energies and the average dimensions of polyribonucleotides. Biopolymers. 11: 25-56. PMID 5008177 DOI: 10.1002/bip.1972.360110103  0.96
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