| Year |
Citation |
Score |
| 2020 |
Lu XJ. DSSR-enabled innovative schematics of 3D nucleic acid structures with PyMOL. Nucleic Acids Research. PMID 32442277 DOI: 10.1093/Nar/Gkaa426 |
0.395 |
|
| 2019 |
Kribelbauer JF, Lu XJ, Rohs R, Mann RS, Bussemaker HJ. Towards a mechanistic understanding of DNA methylation readout by transcription factors. Journal of Molecular Biology. PMID 31689433 DOI: 10.1016/J.Jmb.2019.10.021 |
0.653 |
|
| 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 |
0.475 |
|
| 2019 |
Sharp KA, Lu XJ, Cingolani G, Harvey SC. DNA Conformational Changes Play a Force-Generating Role during Bacteriophage Genome Packaging. Biophysical Journal. PMID 31103227 DOI: 10.1016/J.Bpj.2019.02.034 |
0.401 |
|
| 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 |
0.443 |
|
| 2019 |
Li S, Lu X, Olson WK. A New Web Server for the Identification of Novel Nucleic Acid Structural Motifs and their Interactions with Proteins Biophysical Journal. 116: 289a. DOI: 10.1016/J.Bpj.2018.11.1560 |
0.378 |
|
| 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 |
0.379 |
|
| 2017 |
Hanson RM, Lu XJ. DSSR-enhanced visualization of nucleic acid structures in Jmol. Nucleic Acids Research. PMID 28472503 DOI: 10.1093/Nar/Gkx365 |
0.434 |
|
| 2016 |
Waters JT, Kim HD, Gumbart JC, Lu XJ, Harvey SC. DNA Scrunching in the Packaging of Viral Genomes. The Journal of Physical Chemistry. B. PMID 27214211 DOI: 10.1021/Acs.Jpcb.6B02149 |
0.408 |
|
| 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 |
0.63 |
|
| 2014 |
Fazlollahi M, Lee E, Muroff I, Lu XJ, Gomez-Alcala P, Causton HC, Bussemaker HJ. Harnessing natural sequence variation to dissect posttranscriptional regulatory networks in yeast. G3 (Bethesda, Md.). 4: 1539-53. PMID 24938291 DOI: 10.1534/G3.114.012039 |
0.617 |
|
| 2014 |
Lu X, Olson WK, Bussemaker HJ. SNAP: Software for Analyzing Structures of Nucleic Acid-Protein Complexes Biophysical Journal. 106: 699a. DOI: 10.1016/J.Bpj.2013.11.3867 |
0.669 |
|
| 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 |
0.455 |
|
| 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 |
0.447 |
|
| 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 |
0.411 |
|
| 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 |
0.616 |
|
| 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 |
0.484 |
|
| 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 |
0.435 |
|
| 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 |
0.418 |
|
| 2008 |
Boorsma A, Lu XJ, Zakrzewska A, Klis FM, Bussemaker HJ. Inferring condition-specific modulation of transcription factor activity in yeast through regulon-based analysis of genomewide expression. Plos One. 3: e3112. PMID 18769540 DOI: 10.1371/Journal.Pone.0003112 |
0.592 |
|
| 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 |
0.441 |
|
| 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 |
0.317 |
|
| 2006 |
Moorman C, Sun LV, Wang J, de Wit E, Talhout W, Ward LD, Greil F, Lu XJ, White KP, Bussemaker HJ, van Steensel B. Hotspots of transcription factor colocalization in the genome of Drosophila melanogaster. Proceedings of the National Academy of Sciences of the United States of America. 103: 12027-32. PMID 16880385 DOI: 10.1073/Pnas.0605003103 |
0.613 |
|
| 2006 |
Halasz G, van Batenburg MF, Perusse J, Hua S, Lu XJ, White KP, Bussemaker HJ. Detecting transcriptionally active regions using genomic tiling arrays. Genome Biology. 7: R59. PMID 16859498 DOI: 10.1186/Gb-2006-7-7-R59 |
0.555 |
|
| 2005 |
Covell DG, Wallqvist A, Huang R, Thanki N, Rabow AA, Lu XJ. Linking tumor cell cytotoxicity to mechanism of drug action: an integrated analysis of gene expression, small-molecule screening and structural databases. Proteins. 59: 403-33. PMID 15778971 DOI: 10.1002/Prot.20392 |
0.325 |
|
| 2005 |
McLaughlin WA, Kulp DW, De La Cruz J, Lu XJ, Lawson CL, Berman HM. A structure-based method for identifying DNA-binding proteins and their sites of DNA-interaction Journal of Structural and Functional Genomics. 5: 255-265. PMID 15704013 DOI: 10.1007/S10969-005-4902-1 |
0.443 |
|
| 2004 |
Gardiner EJ, Hunter CA, Lu XJ, Willett P. A structural similarity analysis of double-helical DNA. Journal of Molecular Biology. 343: 879-89. PMID 15476807 DOI: 10.1016/J.Jmb.2004.08.092 |
0.432 |
|
| 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 |
0.501 |
|
| 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 |
0.399 |
|
| 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 |
0.39 |
|
| 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 |
0.408 |
|
| 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 |
0.351 |
|
| 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 |
0.395 |
|
| 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 |
0.45 |
|
| 1997 |
Lu XJ, El Hassan MA, Hunter CA. Structure and conformation of helical nucleic acids: Rebuilding program (SCHNArP) Journal of Molecular Biology. 273: 681-691. PMID 9356256 DOI: 10.1006/Jmbi.1997.1345 |
0.383 |
|
| 1997 |
Lu XJ, El Hassan MA, Hunter CA. Structure and conformation of helical nucleic acids: Analysis program (SCHNAaP) Journal of Molecular Biology. 273: 668-680. PMID 9356255 DOI: 10.1006/Jmbi.1997.1346 |
0.398 |
|
| 1997 |
Hunter CA, Lu XJ. Construction of double-helical DNA structures based on dinucleotide building blocks Journal of Biomolecular Structure and Dynamics. 14: 747-756. PMID 9195343 DOI: 10.1080/07391102.1997.10508177 |
0.415 |
|
| 1997 |
Hunter CA, Lu XJ. DNA base-stacking interactions: A comparison of theoretical calculations with oligonucleotide x-ray crystal structures Journal of Molecular Biology. 265: 603-619. PMID 9048952 DOI: 10.1006/Jmbi.1996.0755 |
0.351 |
|
| 1995 |
Hunter CA, Lu X, Kapteijn GM, van Koten G. Influence of fluorine on aromatic interactions Journal of the Chemical Society, Faraday Transactions. 91: 2009. DOI: 10.1039/Ft9959102009 |
0.303 |
|
| 1993 |
Jacobo-Molina A, Ding J, Nanni RG, Clark AD, Lu X, Tantillo C, Williams RL, Kamer G, Ferris AL, Clark P. Crystal structure of human immunodeficiency virus type 1 reverse transcriptase complexed with double-stranded DNA at 3.0 A resolution shows bent DNA. Proceedings of the National Academy of Sciences of the United States of America. 90: 6320-4. PMID 7687065 DOI: 10.1073/Pnas.90.13.6320 |
0.394 |
|
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