| Year |
Citation |
Score |
| 2023 |
Czarny RS, Ho PS. Thermogenomic Analysis of Left-Handed Z-DNA Propensities in Genomes. Methods in Molecular Biology (Clifton, N.J.). 2651: 195-215. PMID 36892769 DOI: 10.1007/978-1-0716-3084-6_14 |
0.351 |
|
| 2021 |
Ford MC, Rappé AK, Ho PS. A Reduced Generalized Force Field for Biological Halogen Bonds. Journal of Chemical Theory and Computation. PMID 34232642 DOI: 10.1021/acs.jctc.1c00362 |
0.335 |
|
| 2020 |
Vander Zanden CM, Czarny RS, Ho EN, Robertson AB, Ho PS. Structural adaptation of vertebrate endonuclease G for 5-hydroxymethylcytosine recognition and function. Nucleic Acids Research. PMID 32095813 DOI: 10.1093/Nar/Gkaa117 |
0.839 |
|
| 2019 |
Riel AMS, Rowe RK, Ho EN, Carlsson AC, Rappé AK, Berryman OB, Ho PS. Hydrogen Bond Enhanced Halogen Bonds: A Synergistic Interaction in Chemistry and Biochemistry. Accounts of Chemical Research. PMID 31318520 DOI: 10.1021/Acs.Accounts.9B00189 |
0.307 |
|
| 2018 |
Carlsson AC, Scholfield MR, Rowe RK, Ford MC, Alexander AT, Mehl RA, Ho PS. Increasing enzyme stability and activity through hydrogen bond enhanced halogen bonds. Biochemistry. PMID 29921126 DOI: 10.1021/Acs.Biochem.8B00603 |
0.79 |
|
| 2017 |
Ho PS. Structure of the Holliday junction: applications beyond recombination. Biochemical Society Transactions. PMID 28842529 DOI: 10.1042/BST20170048 |
0.457 |
|
| 2017 |
Ford MC, Saxton M, Ho PS. Sulfur as An Acceptor to Bromine in Biomolecular Halogen Bonds. The Journal of Physical Chemistry Letters. PMID 28796521 DOI: 10.1021/acs.jpclett.7b01725 |
0.362 |
|
| 2017 |
Scholfield MR, Ford MC, Carlsson AC, Butta H, Mehl RA, Ho PS. Structure-Energy Relationships of Halogen Bonds in Proteins. Biochemistry. PMID 28345933 DOI: 10.1021/Acs.Biochem.7B00022 |
0.801 |
|
| 2016 |
Vander Zanden CM, Rowe RK, Broad AJ, Robertson AB, Ho PS. The effect of hydroxymethylcytosine on the structure and stability of Holliday junctions. Biochemistry. PMID 27653243 DOI: 10.1021/Acs.Biochem.6B00801 |
0.821 |
|
| 2014 |
Scholfield MR, Ford MC, Vander Zanden CM, Billman MM, Ho PS, Rappé AK. Force Field Model of Periodic Trends in Biomolecular Halogen Bonds. The Journal of Physical Chemistry. B. PMID 25338128 DOI: 10.1021/Jp509003R |
0.785 |
|
| 2013 |
Vander Zanden CM, Carter M, Ho PS. Determining thermodynamic properties of molecular interactions from single crystal studies. Methods (San Diego, Calif.). 64: 12-8. PMID 23933330 DOI: 10.1016/J.Ymeth.2013.07.039 |
0.833 |
|
| 2013 |
Carter M, Voth AR, Scholfield MR, Rummel B, Sowers LC, Ho PS. Enthalpy-entropy compensation in biomolecular halogen bonds measured in DNA junctions. Biochemistry. 52: 4891-903. PMID 23789744 DOI: 10.1021/Bi400590H |
0.796 |
|
| 2013 |
Scholfield MR, Zanden CM, Carter M, Ho PS. Halogen bonding (X-bonding): a biological perspective. Protein Science : a Publication of the Protein Society. 22: 139-52. PMID 23225628 DOI: 10.1002/Pro.2201 |
0.796 |
|
| 2012 |
Carter M, Rappé AK, Ho PS. Scalable Anisotropic Shape and Electrostatic Models for Biological Bromine Halogen Bonds. Journal of Chemical Theory and Computation. 8: 2461-73. PMID 26588975 DOI: 10.1021/Ct3001969 |
0.533 |
|
| 2011 |
Carter M, Ho PS. Assaying the energies of biological halogen bonds Crystal Growth and Design. 11: 5087-5095. DOI: 10.1021/Cg200991V |
0.564 |
|
| 2010 |
Hays FA, Teegarden A, Jones ZJR, Harms M, Raup D, Watson J, Cavaliere E, Ho PS. How sequence defines structure: A crystallographic map of DNA structure and conformation (Proceedings of the National Academy of Sciences of the United States of America (2005) 102 (7157-7162) DOI: 10.1073/pnas.0409455102) Proceedings of the National Academy of Sciences of the United States of America. 107: 4486. DOI: 10.1073/Pnas.1000618107 |
0.703 |
|
| 2009 |
Voth AR, Khuu P, Oishi K, Ho PS. Halogen bonds as orthogonal molecular interactions to hydrogen bonds. Nature Chemistry. 1: 74-9. PMID 21378804 DOI: 10.1038/Nchem.112 |
0.776 |
|
| 2009 |
Ho PS. Detailed mechanism for transposition by TnpA transposase involves DNA shape rather than direct protein-DNA recognition to generate an active nucleoprotein complex. F1000 Biology Reports. 1: 37. PMID 20948648 DOI: 10.3410/B1-37 |
0.35 |
|
| 2009 |
Khuu P, Ho PS. A rare nucleotide base tautomer in the structure of an asymmetric DNA junction. Biochemistry. 48: 7824-32. PMID 19580331 DOI: 10.1021/bi900829b |
0.479 |
|
| 2009 |
Ho PS. Thermogenomics: thermodynamic-based approaches to genomic analyses of DNA structure. Methods (San Diego, Calif.). 47: 159-67. PMID 18848994 DOI: 10.1016/j.ymeth.2008.09.007 |
0.301 |
|
| 2007 |
Voth AR, Ho PS. The role of halogen bonding in inhibitor recognition and binding by protein kinases. Current Topics in Medicinal Chemistry. 7: 1336-48. PMID 17692024 DOI: 10.2174/156802607781696846 |
0.779 |
|
| 2007 |
Voth AR, Hays FA, Ho PS. Directing macromolecular conformation through halogen bonds. Proceedings of the National Academy of Sciences of the United States of America. 104: 6188-93. PMID 17379665 DOI: 10.1073/Pnas.0610531104 |
0.813 |
|
| 2006 |
Khuu PA, Voth AR, Hays FA, Ho PS. The stacked-X DNA Holliday junction and protein recognition. Journal of Molecular Recognition : Jmr. 19: 234-42. PMID 16575941 DOI: 10.1002/Jmr.765 |
0.83 |
|
| 2006 |
Hays FA, Schirf V, Ho PS, Demeler B. Solution formation of Holliday junctions in inverted-repeat DNA sequences. Biochemistry. 45: 2467-71. PMID 16489738 DOI: 10.1021/Bi052129X |
0.758 |
|
| 2005 |
Hays FA, Teegarden A, Jones ZJ, Harms M, Raup D, Watson J, Cavaliere E, Ho PS. How sequence defines structure: a crystallographic map of DNA structure and conformation. Proceedings of the National Academy of Sciences of the United States of America. 102: 7157-62. PMID 15870206 DOI: 10.1073/Pnas.0409455102 |
0.75 |
|
| 2004 |
Champ PC, Maurice S, Vargason JM, Camp T, Ho PS. Distributions of Z-DNA and nuclear factor I in human chromosome 22: a model for coupled transcriptional regulation. Nucleic Acids Research. 32: 6501-10. PMID 15598822 DOI: 10.1093/Nar/Gkh988 |
0.789 |
|
| 2004 |
Auffinger P, Hays FA, Westhof E, Ho PS. Halogen bonds in biological molecules. Proceedings of the National Academy of Sciences of the United States of America. 101: 16789-94. PMID 15557000 DOI: 10.1073/Pnas.0407607101 |
0.672 |
|
| 2004 |
Hays FA, Jones ZJ, Ho PS. Influence of minor groove substituents on the structure of DNA Holliday junctions. Biochemistry. 43: 9813-22. PMID 15274635 DOI: 10.1021/Bi049461D |
0.769 |
|
| 2004 |
Watson J, Hays FA, Ho PS. Definitions and analysis of DNA Holliday junction geometry. Nucleic Acids Research. 32: 3017-27. PMID 15173384 DOI: 10.1093/Nar/Gkh631 |
0.735 |
|
| 2003 |
Hays FA, Watson J, Ho PS. Caution! DNA crossing: crystal structures of Holliday junctions. The Journal of Biological Chemistry. 278: 49663-6. PMID 14563836 DOI: 10.1074/Jbc.R300033200 |
0.728 |
|
| 2003 |
Hays FA, Vargason JM, Ho PS. Effect of sequence on the conformation of DNA holliday junctions. Biochemistry. 42: 9586-97. PMID 12911300 DOI: 10.1021/Bi0346603 |
0.842 |
|
| 2002 |
Eichman BF, Ortiz-Lombardía M, Aymamí J, Coll M, Ho PS. The inherent properties of DNA four-way junctions: comparing the crystal structures of holliday junctions. Journal of Molecular Biology. 320: 1037-51. PMID 12126623 DOI: 10.1016/S0022-2836(02)00540-5 |
0.752 |
|
| 2002 |
Vargason JM, Ho PS. The effect of cytosine methylation on the structure and geometry of the Holliday junction: the structure of d(CCGGTACm5CGG) at 1.5 A resolution. The Journal of Biological Chemistry. 277: 21041-9. PMID 11919197 DOI: 10.1074/Jbc.M201357200 |
0.821 |
|
| 2001 |
Ho PS, Eichman BF. The crystal structures of DNA Holliday junctions. Current Opinion in Structural Biology. 11: 302-8. PMID 11406378 DOI: 10.1016/S0959-440X(00)00219-0 |
0.713 |
|
| 2001 |
Vargason JM, Henderson K, Ho PS. A crystallographic map of the transition from B-DNA to A-DNA. Proceedings of the National Academy of Sciences of the United States of America. 98: 7265-70. PMID 11390969 DOI: 10.1073/Pnas.121176898 |
0.83 |
|
| 2001 |
Eichman BF, Mooers BH, Alberti M, Hearst JE, Ho PS. The crystal structures of psoralen cross-linked DNAs: drug-dependent formation of Holliday junctions. Journal of Molecular Biology. 308: 15-26. PMID 11302703 DOI: 10.1006/Jmbi.2001.4567 |
0.838 |
|
| 2001 |
Bash RC, Vargason JM, Cornejo S, Ho PS, Lohr D. Intrinsically bent DNA in the promoter regions of the yeast GAAL1-10 and GAL80 genes. The Journal of Biological Chemistry. 276: 861-6. PMID 11013248 DOI: 10.1074/Jbc.M007070200 |
0.792 |
|
| 2001 |
Vargason JM, Ho PS. Response to NG and Dickerson Nature Structural Biology. 8: 107-108. DOI: 10.1038/84081 |
0.828 |
|
| 2000 |
Vargason JM, Eichman BF, Ho PS. The extended and eccentric E-DNA structure induced by cytosine methylation or bromination. Nature Structural Biology. 7: 758-61. PMID 10966645 DOI: 10.1038/78985 |
0.831 |
|
| 2000 |
Eichman BF, Vargason JM, Mooers BH, Ho PS. The Holliday junction in an inverted repeat DNA sequence: sequence effects on the structure of four-way junctions. Proceedings of the National Academy of Sciences of the United States of America. 97: 3971-6. PMID 10760268 DOI: 10.1073/Pnas.97.8.3971 |
0.843 |
|
| 1999 |
Eichman BF, Schroth GP, Basham BE, Ho PS. The intrinsic structure and stability of out-of-alternation base pairs in Z-DNA. Nucleic Acids Research. 27: 543-50. PMID 9862978 DOI: 10.1093/Nar/27.2.543 |
0.817 |
|
| 1997 |
Ho PS, Mooers BH. Z-DNA crystallography . Biopolymers. 14: 65-90. PMID 19174848 DOI: 10.1002/(SICI)1097-0282(1997)44:1<65::AID-BIP5>3.0.CO;2-Y |
0.802 |
|
| 1997 |
Mooers BH, Eichman BF, Ho PS. The structures and relative stabilities of d(G x G) reverse Hoogsteen, d(G x T) reverse wobble, and d(G x C) reverse Watson-Crick base-pairs in DNA crystals. Journal of Molecular Biology. 269: 796-810. PMID 9223642 DOI: 10.1006/jmbi.1997.1100 |
0.802 |
|
| 1996 |
Howell ML, Schroth GP, Ho PS. Sequence-dependent effects of spermine on the thermodynamics of the B-DNA to Z-DNA transition. Biochemistry. 35: 15373-82. PMID 8952489 DOI: 10.1021/bi961881i |
0.752 |
|
| 1996 |
Rasmussen C, Leisy DJ, Ho PS, Rohrmann GF. Structure-function analysis of the Autographa californica multinucleocapsid nuclear polyhedrosis virus homologous region palindromes. Virology. 224: 235-45. PMID 8862418 DOI: 10.1006/Viro.1996.0525 |
0.426 |
|
| 1995 |
Basham B, Schroth GP, Ho PS. An A-DNA triplet code: thermodynamic rules for predicting A- and B-DNA. Proceedings of the National Academy of Sciences of the United States of America. 92: 6464-8. PMID 7604014 DOI: 10.1073/Pnas.92.14.6464 |
0.829 |
|
| 1995 |
Mooers BH, Schroth GP, Baxter WW, Ho PS. Alternating and non-alternating dG-dC hexanucleotides crystallize as canonical A-DNA. Journal of Molecular Biology. 249: 772-84. PMID 7602589 DOI: 10.1006/Jmbi.1995.0336 |
0.85 |
|
| 1995 |
Schroth GP, Ho PS. Occurrence of potential cruciform and H-DNA forming sequences in genomic DNA. Nucleic Acids Research. 23: 1977-83. PMID 7596826 DOI: 10.1093/Nar/23.11.1977 |
0.726 |
|
| 1994 |
Ho PS. The non-B-DNA structure of d(CA/TG)n does not differ from that of Z-DNA. Proceedings of the National Academy of Sciences of the United States of America. 91: 9549-53. PMID 7937803 DOI: 10.1073/Pnas.91.20.9549 |
0.363 |
|
| 1993 |
Kagawa TF, Howell ML, Tseng K, Ho PS. Effects of base substituents on the hydration of B- and Z-DNA: correlations to the B- to Z-DNA transition. Nucleic Acids Research. 21: 5978-86. PMID 8290360 |
0.842 |
|
| 1993 |
Schroth GP, Kagawa TF, Ho PS. Structure and thermodynamics of nonalternating C.G base pairs in Z-DNA: the 1.3-A crystal structure of the asymmetric hexanucleotide d(m5CGGGm5CG).d(m5CGCCm5CG). Biochemistry. 32: 13381-92. PMID 8257675 DOI: 10.2210/Pdb145D/Pdb |
0.828 |
|
| 1992 |
Schroth GP, Chou PJ, Ho PS. Mapping Z-DNA in the human genome. Computer-aided mapping reveals a nonrandom distribution of potential Z-DNA-forming sequences in human genes. The Journal of Biological Chemistry. 267: 11846-55. PMID 1601856 |
0.738 |
|
| 1992 |
Schroth GP, Siino JS, Cooney CA, Th'ng JP, Ho PS, Bradbury EM. Intrinsically bent DNA flanks both sides of an RNA polymerase I transcription start site. Both regions display novel electrophoretic mobility. The Journal of Biological Chemistry. 267: 9958-64. PMID 1577826 |
0.744 |
|
| 1991 |
Ho PS, Kagawa TF, Tseng KH, Schroth GP, Zhou GW. Prediction of a crystallization pathway for Z-DNA hexanucleotides. Science (New York, N.Y.). 254: 1003-6. PMID 1948069 DOI: 10.1126/Science.1948069 |
0.812 |
|
| 1991 |
Geierstanger BH, Kagawa TF, Chen SL, Quigley GJ, Ho PS. Base-specific binding of copper(II) to Z-DNA. The 1.3-A single crystal structure of d(m5CGUAm5CG) in the presence of CuCl2. The Journal of Biological Chemistry. 266: 20185-91. PMID 1939079 DOI: 10.2210/Pdb1D40/Pdb |
0.815 |
|
| 1991 |
Kagawa TF, Geierstanger BH, Wang AH, Ho PS. Covalent modification of guanine bases in double-stranded DNA. The 1.2-A Z-DNA structure of d(CGCGCG) in the presence of CuCl2. The Journal of Biological Chemistry. 266: 20175-84. PMID 1939078 DOI: 10.2210/Pdb1D39/Pdb |
0.83 |
|
| 1990 |
Zhou G, Ho PS. Stabilization of Z-DNA by demethylation of thymine bases: 1.3-Å single-crystal structure of d(m5CGUAm5CG) Biochemistry. 29: 7229-7236. PMID 2207101 DOI: 10.1021/Bi00483A010 |
0.464 |
|
| 1990 |
Green SA, Simpson DJ, Zhou G, Ho PS, Blough NV. Intramolecular quenching of excited singlet states by stable nitroxyl radicals Journal of the American Chemical Society. 112: 7337-7346. DOI: 10.1021/Ja00176A038 |
0.525 |
|
| 1989 |
Kagawa TF, Stoddard D, Zhou GW, Ho PS. Quantitative analysis of DNA secondary structure from solvent-accessible surfaces: the B- to Z-DNA transition as a model. Biochemistry. 28: 6642-51. PMID 2790019 DOI: 10.1021/Bi00442A017 |
0.811 |
|
| 1988 |
Ho PS, Quigley GJ, Tilton RF, Rich A. Hydration of methylated and nonmethylated B-DNA and Z-DNA Journal of Physical Chemistry. 92: 939-945. |
0.358 |
|
| 1987 |
Ellison MJ, Fenton MJ, Ho PS, Rich A. Long-range interactions of multiple DNA structural transitions within a common topological domain. The Embo Journal. 6: 1513-22. PMID 3608986 DOI: 10.1002/J.1460-2075.1987.Tb02394.X |
0.669 |
|
| 1987 |
Ho PS, Frederick CA, Saal D, Wang AH, Rich A. The interactions of ruthenium hexaammine with Z-DNA: crystal structure of a Ru(NH3)6+3 salt of d(CGCGCG) at 1.2 A resolution. Journal of Biomolecular Structure & Dynamics. 4: 521-34. PMID 3271453 DOI: 10.1080/07391102.1987.10507657 |
0.691 |
|
| 1986 |
Ho PS, Ellison MJ, Quigley GJ, Rich A. A computer aided thermodynamic approach for predicting the formation of Z-DNA in naturally occurring sequences. The Embo Journal. 5: 2737-44. PMID 3780676 DOI: 10.1002/J.1460-2075.1986.Tb04558.X |
0.661 |
|
| 1986 |
Kelleher RJ, Ellison MJ, Ho PS, Rich A. Competitive behavior of multiple, discrete B-Z transitions in supercoiled DNA. Proceedings of the National Academy of Sciences of the United States of America. 83: 6342-6. PMID 3462699 DOI: 10.1073/Pnas.83.17.6342 |
0.658 |
|
| 1986 |
Liang N, Kang CH, Ho PS, Margoliash E, Hoffman BM. Long-range electron transfer from iron(II)-cytochrome c to (zinc-cytochrome c peroxidase)(+) within the 1:1 complex Journal of the American Chemical Society. 108: 4665-4666. |
0.456 |
|
| 1985 |
Ho PS, Frederick CA, Quigley GJ, van der Marel GA, van Boom JH, Wang AH, Rich A. G.T wobble base-pairing in Z-DNA at 1.0 A atomic resolution: the crystal structure of d(CGCGTG). The Embo Journal. 4: 3617-23. PMID 4092690 DOI: 10.1002/J.1460-2075.1985.Tb04125.X |
0.692 |
|
| 1985 |
Peterson-Kennedy SE, McGourty JL, Ho PS, Sutoris CJ, Liang N, Zemel H, Blough NV, Margoliash E, Hoffman BM. Long-Range Electron Transfer at Fixed and Known Distance within Protein Complexes Coordination Chemistry Reviews. 64: 125-133. DOI: 10.1016/0010-8545(85)80046-1 |
0.649 |
|
| 1985 |
Ho PS, Sutoris C, Liang N, Margoliash E, Hoffman BM. Species specificity of long-range electron transfer within the complex between zinc-substituted cytochrome c peroxidase and cytochrome c Journal of the American Chemical Society. 107: 1070-1071. |
0.464 |
|
| 1984 |
Ho PS, Hoffman BM, Solomon N, Kang CH, Margoliash E. Kinetics and energetics of intramolecular electron transfer in yeast cytochrome c peroxidase. Biochemistry. 23: 4122-8. PMID 6091738 DOI: 10.1021/Bi00313A017 |
0.493 |
|
| 1983 |
Martinsen J, Irwin MJ, Ho PS, Hoffman BM, Klotz IM. Oxidation state of binuclear iron site in azidosemimethemerythrin. Biochemical and Biophysical Research Communications. 112: 954-6. PMID 6303342 DOI: 10.1016/0006-291X(83)91710-2 |
0.444 |
|
| 1983 |
Ho PS, Hoffman BM, Kang CH, Margoliash E. Control of the transfer of oxidizing equivalents between heme iron and free radical site in yeast cytochrome c peroxidase. The Journal of Biological Chemistry. 258: 4356-63. PMID 6300084 |
0.477 |
|
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